<?xml version="1.0" encoding="us-ascii"?><InstanceReport xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"><Version>2.4.0.8</Version><ReportLongName>112 - Disclosure - Shareholders' Equity</ReportLongName><DisplayLabelColumn>true</DisplayLabelColumn><ShowElementNames>false</ShowElementNames><RoundingOption /><HasEmbeddedReports>false</HasEmbeddedReports><Columns><Column FlagID="0"><Id>1</Id><IsAbstractGroupTitle>false</IsAbstractGroupTitle><LabelSeparator>

</LabelSeparator><CurrencyCode /><FootnoteIndexer /><hasSegments>false</hasSegments><hasScenarios>false</hasScenarios><MCU><KeyName /><CurrencySymbol /><contextRef><ContextID>P01_01_2013To06_30_2013</ContextID><EntitySchema>http://www.sec.gov/CIK</EntitySchema><EntityValue>0000826683</EntityValue><PeriodDisplayName /><PeriodType>duration</PeriodType><PeriodStartDate>2013-01-01T00:00:00</PeriodStartDate><PeriodEndDate>2013-06-30T00:00:00</PeriodEndDate><Segments /><Scenarios /></contextRef><UPS /><CurrencyCode /><OriginalCurrencyCode /></MCU><CurrencySymbol /><Labels><Label Key="CalendarSupplement" Id="0" Label="6 Months Ended" /><Label Key="Calendar" Id="1" Label="Jun. 30, 2013" /></Labels></Column></Columns><Rows><Row FlagID="0"><Id>1</Id><IsAbstractGroupTitle>true</IsAbstractGroupTitle><LabelSeparator>

</LabelSeparator><Level>1</Level><ElementName>us-gaap_StockholdersEquityNoteAbstract</ElementName><ElementPrefix>us-gaap_</ElementPrefix><IsBaseElement>true</IsBaseElement><BalanceType>na</BalanceType><PeriodType>duration</PeriodType><IsReportTitle>false</IsReportTitle><IsSegmentTitle>false</IsSegmentTitle><IsCalendarTitle>false</IsCalendarTitle><IsEquityPrevioslyReportedAsRow>false</IsEquityPrevioslyReportedAsRow><IsEquityAdjustmentRow>false</IsEquityAdjustmentRow><IsBeginningBalance>false</IsBeginningBalance><IsEndingBalance>false</IsEndingBalance><IsReverseSign>false</IsReverseSign><FootnoteIndexer /><Cells><Cell FlagID="0" ContextID="" UnitID=""><Id>1</Id><IsNumeric>false</IsNumeric><IsRatio>false</IsRatio><DisplayZeroAsNone>false</DisplayZeroAsNone><NumericAmount>0</NumericAmount><RoundedNumericAmount>0</RoundedNumericAmount><NonNumbericText /><FootnoteIndexer /><CurrencyCode /><CurrencySymbol /><IsIndependantCurrency>false</IsIndependantCurrency><ShowCurrencySymbol>false</ShowCurrencySymbol><DisplayDateInUSFormat>false</DisplayDateInUSFormat></Cell></Cells><ElementDataType>xbrli:stringItemType</ElementDataType><SimpleDataType>string</SimpleDataType><IsTotalLabel>false</IsTotalLabel><UnitID>0</UnitID><Label>Stockholders' Equity Note [Abstract]</Label></Row><Row FlagID="0"><Id>2</Id><IsAbstractGroupTitle>false</IsAbstractGroupTitle><LabelSeparator>

</LabelSeparator><Level>2</Level><ElementName>us-gaap_StockholdersEquityNoteDisclosureTextBlock</ElementName><ElementPrefix>us-gaap_</ElementPrefix><IsBaseElement>true</IsBaseElement><BalanceType>na</BalanceType><PeriodType>duration</PeriodType><IsReportTitle>false</IsReportTitle><IsSegmentTitle>false</IsSegmentTitle><IsCalendarTitle>false</IsCalendarTitle><IsEquityPrevioslyReportedAsRow>false</IsEquityPrevioslyReportedAsRow><IsEquityAdjustmentRow>false</IsEquityAdjustmentRow><IsBeginningBalance>false</IsBeginningBalance><IsEndingBalance>false</IsEndingBalance><IsReverseSign>false</IsReverseSign><PreferredLabelRole>label</PreferredLabelRole><FootnoteIndexer /><Cells><Cell FlagID="0" ContextID="P01_01_2013To06_30_2013" UnitID=""><Id>1</Id><IsNumeric>false</IsNumeric><IsRatio>false</IsRatio><DisplayZeroAsNone>false</DisplayZeroAsNone><NumericAmount>0</NumericAmount><RoundedNumericAmount>0</RoundedNumericAmount><NonNumbericText>              &lt;div style="clear:both; FONT-FAMILY:Times New Roman;FONT-SIZE: 10pt;MARGIN: 0pt 0px; FONT: 10pt Times New Roman, Times, Serif "&gt;  &lt;div style="clear:both; FONT-FAMILY:Times New Roman;FONT-SIZE: 10pt;MARGIN: 0pt 0px; FONT: 10pt Times New Roman, Times, Serif"&gt;  &lt;b&gt;6.&amp;#160;&amp;#160;Shareholders&amp;#8217; Equity&lt;/b&gt;&lt;/div&gt;    &lt;div style="clear:both; FONT-FAMILY:Times New Roman;FONT-SIZE: 10pt;MARGIN: 0pt 0px; FONT: 10pt Times New Roman, Times, Serif"&gt;  &amp;#160;&lt;/div&gt;    &lt;div style="clear:both; FONT-FAMILY:Times New Roman;FONT-SIZE: 10pt;MARGIN: 0pt 0px; FONT: 10pt Times New Roman, Times, Serif"&gt;  &lt;b&gt;&lt;i&gt;Sale of Common Stock&lt;/i&gt;&lt;/b&gt;&lt;/div&gt;    &lt;div style="clear:both; FONT-FAMILY:Times New Roman;FONT-SIZE: 10pt;TEXT-INDENT: 0.75in; MARGIN: 0pt 0px; FONT: 10pt Times New Roman, Times, Serif"&gt;  &amp;#160;&lt;/div&gt;    &lt;div style="clear:both; FONT-FAMILY:Times New Roman;FONT-SIZE: 10pt;TEXT-INDENT: 0.5in; MARGIN: 0pt 0px; FONT: 10pt Times New Roman, Times, Serif"&gt;  On March 28, 2013 and April 26, 2013, the Company entered into a  definitive agreement (the &amp;#8220;Stock Purchase Agreement&amp;#8221;)  for the sale and issuance of &lt;font style=" FONT-SIZE: 10pt"&gt;  60,745,824&lt;/font&gt; common shares at $&lt;font style=" FONT-SIZE: 10pt"&gt;0.03&lt;/font&gt; per share, resulting in total  proceeds to the Company of $&lt;font style=" FONT-SIZE: 10pt"&gt;1,822,375&lt;/font&gt;. For every four common shares  purchased, the investors received a warrant to purchase one share  of common stock at $&lt;font style=" FONT-SIZE: 10pt"&gt;0.04&lt;/font&gt; per  share, for a term of&amp;#160;&lt;font style=" FONT-SIZE: 10pt"&gt;five  years&lt;/font&gt;. A total of &lt;font style=" FONT-SIZE: 10pt"&gt;  15,186,454&lt;/font&gt; warrants were issued.&lt;/div&gt;    &lt;div style="clear:both; FONT-FAMILY:Times New Roman;FONT-SIZE: 10pt;TEXT-INDENT: 0.5in; MARGIN: 0pt 0px; FONT: 10pt Times New Roman, Times, Serif"&gt;  &amp;#160;&lt;/div&gt;    &lt;div style="clear:both; FONT-FAMILY:Times New Roman;FONT-SIZE: 10pt;TEXT-INDENT: 0.5in; MARGIN: 0pt 0px; FONT: 10pt Times New Roman, Times, Serif"&gt;  The total proceeds of $&lt;font style=" FONT-SIZE: 10pt"&gt;1,822,375&lt;/font&gt; is accounted for as an issuance  of common stock with warrants and was allocated to the individual  instruments based on the relative fair value of each instrument at  the time of issuance.&amp;#160;Based on such allocation method, the  values allocated to common stock and warrants were $&lt;font style=" FONT-SIZE: 10pt"&gt;1,466,000&lt;/font&gt; and $&lt;font style=" FONT-SIZE: 10pt"&gt;356,000&lt;/font&gt;, respectively.&lt;/div&gt;    &lt;div style="clear:both; FONT-FAMILY:Times New Roman;FONT-SIZE: 10pt;MARGIN: 0pt 0px; FONT: 10pt Times New Roman, Times, Serif"&gt;  &lt;b&gt;&lt;i&gt;&amp;#160;&lt;/i&gt;&lt;/b&gt;&lt;/div&gt;    &lt;div style="clear:both; FONT-FAMILY:Times New Roman;FONT-SIZE: 10pt;MARGIN: 0pt 0px; FONT: 10pt Times New Roman, Times, Serif"&gt;  &lt;b&gt;&lt;i&gt;Conversion of Series D and E Convertible Preferred Stock to  Common Stock&lt;/i&gt;&lt;/b&gt;&lt;/div&gt;    &lt;div style="clear:both; FONT-FAMILY:Times New Roman;FONT-SIZE: 10pt;TEXT-INDENT: 0.75in; MARGIN: 0pt 0px; FONT: 10pt Times New Roman, Times, Serif"&gt;  &amp;#160;&lt;/div&gt;    &lt;div style="clear:both; FONT-FAMILY:Times New Roman;FONT-SIZE: 10pt;TEXT-INDENT: 0.5in; MARGIN: 0pt 0px; FONT: 10pt Times New Roman, Times, Serif"&gt;  In connection with the sale of common stock described above, the  Investors Rights Agreement dated September 9, 2009 by and among the  Company and investors in its Series D Convertible Preferred Stock  was terminated and a new Voting Agreement dated March 28, 2013 was  entered into.&lt;/div&gt;    &lt;div style="clear:both; FONT-FAMILY:Times New Roman;FONT-SIZE: 10pt;TEXT-INDENT: 0.75in; MARGIN: 0pt 0px; FONT: 10pt Times New Roman, Times, Serif"&gt;  &amp;#160;&lt;/div&gt;    &lt;div style="clear:both; FONT-FAMILY:Times New Roman;FONT-SIZE: 10pt;TEXT-INDENT: 0.5in; MARGIN: 0pt 0px; FONT: 10pt Times New Roman, Times, Serif"&gt;  On March 28, 2013, all outstanding shares of Series D and Series E  Convertible Preferred Stock of the Company were converted into  shares of common stock. Each share of Series D Convertible  Preferred Stock was converted into &lt;font style=" FONT-SIZE: 10pt"&gt;  0.34127&lt;/font&gt; share of common stock. Each share of Series E  Convertible Preferred Stock was converted into one share of common  stock. At the time of the conversion, all dividends accumulated but  not declared on the Series D and series E Convertible Preferred  Stock were canceled.&lt;/div&gt;    &lt;div style="clear:both; FONT-FAMILY:Times New Roman;FONT-SIZE: 10pt;MARGIN: 0pt 0px; FONT: 10pt Times New Roman, Times, Serif"&gt;  &lt;b&gt;&amp;#160;&lt;/b&gt;&lt;/div&gt;    &lt;div style="clear:both; FONT-FAMILY:Times New Roman;FONT-SIZE: 10pt;TEXT-INDENT: 0.5in; MARGIN: 0pt 0px; FONT: 10pt Times New Roman, Times, Serif"&gt;  On March 28, 2013, &lt;font style=" FONT-SIZE: 10pt"&gt;17,001,579&lt;/font&gt;  shares of Series D Convertible Preferred Stock and &lt;font style=" FONT-SIZE: 10pt"&gt;6,303,799&lt;/font&gt; shares of Series E Convertible  Preferred Stock were converted into &lt;font style=" FONT-SIZE: 10pt"&gt;  5,802,126&lt;/font&gt; and &lt;font style=" FONT-SIZE: 10pt"&gt;  6,303,799&lt;/font&gt; shares of common stock, respectively.&lt;/div&gt;  &lt;/div&gt;        </NonNumbericText><FootnoteIndexer /><CurrencyCode /><CurrencySymbol /><IsIndependantCurrency>false</IsIndependantCurrency><ShowCurrencySymbol>false</ShowCurrencySymbol><DisplayDateInUSFormat>false</DisplayDateInUSFormat></Cell></Cells><ElementDataType>nonnum:textBlockItemType</ElementDataType><SimpleDataType>na</SimpleDataType><ElementDefenition>The entire disclosure for shareholders' equity comprised of portions attributable to the parent entity and noncontrolling interest, including other comprehensive income. Includes, but is not limited to, balances of common stock, preferred stock, additional paid-in capital, other capital and retained earnings, accumulated balance for each classification of other comprehensive income and amount of comprehensive income.</ElementDefenition><ElementReferences>Reference 1: http://www.xbrl.org/2003/role/presentationRef

 -Publisher FASB

 -Name Accounting Standards Codification

 -Topic 210

 -SubTopic 10

 -Section S99

 -Paragraph 1

 -Subparagraph (SX 210.5-02.29-31)

 -URI http://asc.fasb.org/extlink&amp;oid=6877327&amp;loc=d3e13212-122682



Reference 2: http://www.xbrl.org/2003/role/presentationRef

 -Publisher FASB

 -Name Accounting Standards Codification

 -Topic 505

 -SubTopic 10

 -Section 50

 -Paragraph 6

 -URI http://asc.fasb.org/extlink&amp;oid=6928386&amp;loc=d3e21506-112644



Reference 3: http://www.xbrl.org/2003/role/presentationRef

 -Publisher SEC

 -Name Regulation S-X (SX)

 -Number 210

 -Section 02

 -Paragraph 29, 30, 31

 -Article 5



Reference 4: http://www.xbrl.org/2003/role/presentationRef

 -Publisher FASB

 -Name Accounting Standards Codification

 -Topic 310

 -SubTopic 10

 -Section S99

 -Paragraph 2

 -Subparagraph (SAB TOPIC 4.E)

 -URI http://asc.fasb.org/extlink&amp;oid=27010918&amp;loc=d3e74512-122707



Reference 5: http://www.xbrl.org/2003/role/presentationRef

 -Publisher FASB

 -Name Accounting Standards Codification

 -Topic 505

 -SubTopic 10

 -Section S99

 -Paragraph 4

 -Subparagraph (SAB TOPIC 4.C)

 -URI http://asc.fasb.org/extlink&amp;oid=27012166&amp;loc=d3e187143-122770



Reference 6: http://www.xbrl.org/2003/role/presentationRef

 -Publisher SEC

 -Name Regulation S-X (SX)

 -Number 210

 -Section 08

 -Article 4



Reference 7: http://www.xbrl.org/2003/role/presentationRef

 -Publisher SEC

 -Name Staff Accounting Bulletin (SAB)

 -Number Topic 4

 -Section C



Reference 8: http://www.xbrl.org/2003/role/presentationRef

 -Publisher SEC

 -Name Staff Accounting Bulletin (SAB)

 -Number Topic 4

 -Section E



Reference 9: http://www.xbrl.org/2003/role/presentationRef

 -Publisher FASB

 -Name Accounting Standards Codification

 -Topic 235

 -SubTopic 10

 -Section S99

 -Paragraph 1

 -Subparagraph (SX 210.4-08.(d),(e))

 -URI http://asc.fasb.org/extlink&amp;oid=26873400&amp;loc=d3e23780-122690



Reference 10: http://www.xbrl.org/2003/role/presentationRef

 -Publisher FASB

 -Name Accounting Standards Codification

 -Glossary Preferred Stock

 -URI http://asc.fasb.org/extlink&amp;oid=6521494



Reference 11: http://www.xbrl.org/2003/role/presentationRef

 -Publisher SEC

 -Name Regulation S-X (SX)

 -Number 210

 -Section 04

 -Article 3



Reference 12: http://www.xbrl.org/2003/role/presentationRef

 -Publisher FASB

 -Name Accounting Standards Codification

 -Topic 505

 -SubTopic 10

 -Section 50

 -Paragraph 2

 -URI http://asc.fasb.org/extlink&amp;oid=6928386&amp;loc=d3e21463-112644



Reference 13: http://www.xbrl.org/2003/role/presentationRef

 -Publisher FASB

 -Name Accounting Standards Codification

 -Topic 505

 -SubTopic 10

 -Section S99

 -Paragraph 1

 -Subparagraph (SX 210.3-04)

 -URI http://asc.fasb.org/extlink&amp;oid=27012166&amp;loc=d3e187085-122770



Reference 14: http://www.xbrl.org/2003/role/presentationRef

 -Publisher FASB

 -Name Accounting Standards Codification

 -Topic 505

 -SubTopic 10

 -Section 50

 -Paragraph 3

 -URI http://asc.fasb.org/extlink&amp;oid=6928386&amp;loc=d3e21475-112644



Reference 15: http://www.xbrl.org/2003/role/presentationRef

 -Publisher FASB

 -Name Accounting Standards Codification

 -Topic 505

 -SubTopic 10

 -Section 50

 -Paragraph 11

 -URI http://asc.fasb.org/extlink&amp;oid=6928386&amp;loc=d3e21564-112644



Reference 16: http://www.xbrl.org/2003/role/presentationRef

 -Publisher FASB

 -Name Accounting Standards Codification

 -Topic 505

 -SubTopic 10

 -Section 50

 -Paragraph 5

 -URI http://asc.fasb.org/extlink&amp;oid=6928386&amp;loc=d3e21488-112644



Reference 17: http://www.xbrl.org/2003/role/presentationRef

 -Publisher FASB

 -Name Accounting Standards Codification

 -Topic 505

 -SubTopic 10

 -Section 50

 -Paragraph 4

 -URI http://asc.fasb.org/extlink&amp;oid=6928386&amp;loc=d3e21484-112644



Reference 18: http://www.xbrl.org/2003/role/presentationRef

 -Publisher SEC

 -Name Regulation S-X (SX)

 -Number 210

 -Section 08

 -Paragraph d

 -Article 4



Reference 19: http://www.xbrl.org/2003/role/presentationRef

 -Publisher FASB

 -Name Accounting Standards Codification

 -Topic 505

 -SubTopic 30

 -Section 50

 -Paragraph 2

 -URI http://asc.fasb.org/extlink&amp;oid=6405834&amp;loc=d3e23285-112656



</ElementReferences><IsTotalLabel>false</IsTotalLabel><UnitID>0</UnitID><Label>Stockholders Equity Note Disclosure [Text Block]</Label></Row></Rows><Footnotes /><IsEquityReport>false</IsEquityReport><ReportName>Shareholders' Equity</ReportName><MonetaryRoundingLevel>UnKnown</MonetaryRoundingLevel><SharesRoundingLevel>UnKnown</SharesRoundingLevel><PerShareRoundingLevel>UnKnown</PerShareRoundingLevel><ExchangeRateRoundingLevel>UnKnown</ExchangeRateRoundingLevel><HasCustomUnits>true</HasCustomUnits><IsEmbedReport>false</IsEmbedReport><IsMultiCurrency>false</IsMultiCurrency><ReportType>Sheet</ReportType><RoleURI>http://www.merrimanco.com/role/ShareholdersEquity</RoleURI><NumberOfCols>1</NumberOfCols><NumberOfRows>2</NumberOfRows></InstanceReport>
