<?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>117 - Disclosure - Income Taxes</ReportLongName><DisplayLabelColumn>true</DisplayLabelColumn><ShowElementNames>false</ShowElementNames><RoundingOption /><HasEmbeddedReports>false</HasEmbeddedReports><Columns><Column FlagID="0"><Id>1</Id><IsAbstractGroupTitle>false</IsAbstractGroupTitle><LabelSeparator>

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</LabelSeparator><Level>1</Level><ElementName>us-gaap_IncomeTaxDisclosureAbstract</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>Income Tax Disclosure [Abstract]</Label></Row><Row FlagID="0"><Id>2</Id><IsAbstractGroupTitle>false</IsAbstractGroupTitle><LabelSeparator>

</LabelSeparator><Level>2</Level><ElementName>us-gaap_IncomeTaxDisclosureTextBlock</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>verboseLabel</PreferredLabelRole><FootnoteIndexer /><Cells><Cell FlagID="0" ContextID="P10_01_2012To06_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;TEXT-ALIGN: justify; MARGIN: 0pt 0px; FONT: 10pt Times New Roman, Times, Serif"&gt;  &lt;strong&gt;Note 11 - Income Taxes&lt;/strong&gt;&lt;/div&gt;    &lt;div style="clear:both; FONT-FAMILY:Times New Roman;FONT-SIZE: 10pt"&gt;&lt;font  size="2"&gt;&amp;#160;&lt;/font&gt;&lt;/div&gt;    &lt;div style="clear:both; FONT-FAMILY:Times New Roman;FONT-SIZE: 10pt;TEXT-ALIGN: justify; MARGIN: 0pt 0px; FONT: 10pt Times New Roman, Times, Serif"&gt;  Dynasil Corporation of America and its wholly-owned U.S.  subsidiaries file a consolidated federal income tax return and  various state returns. The Company&amp;#8217;s U.K. subsidiary files  tax returns in the U.K.&lt;/div&gt;    &lt;div style="clear:both; FONT-FAMILY:Times New Roman;FONT-SIZE: 10pt"&gt;&lt;font  size="2"&gt;&amp;#160;&lt;/font&gt;&lt;/div&gt;    &lt;div style="clear:both; FONT-FAMILY:Times New Roman;FONT-SIZE: 10pt;TEXT-ALIGN: justify; MARGIN: 0pt 0px; FONT: 10pt Times New Roman, Times, Serif"&gt;  The Company uses the asset and liability approach to account for  income taxes. Under this approach, deferred income taxes reflect  the net tax effects of temporary differences between the carrying  amounts of assets and liabilities for financial reporting purposes  and the amounts used for income tax purposes and net operating loss  and tax credit carryforwards. The amount of deferred taxes on these  temporary differences is determined using the tax rates that are  expected to apply to the period when the asset is realized or the  liability is settled, as applicable, based on tax rates, and tax  laws, in the respective tax jurisdiction then in effect.&lt;/div&gt;    &lt;div style="clear:both; FONT-FAMILY:Times New Roman;FONT-SIZE: 10pt"&gt;&lt;font  size="2"&gt;&amp;#160;&lt;/font&gt;&lt;/div&gt;    &lt;div style="clear:both; FONT-FAMILY:Times New Roman;FONT-SIZE: 10pt;TEXT-ALIGN: justify; MARGIN: 0pt 0px; FONT: 10pt Times New Roman, Times, Serif"&gt;  In assessing the ability to realize the net deferred tax assets,  management considers various factors including taxable income in  carryback years, future reversals of existing taxable temporary  differences, tax planning strategies and projections of future  taxable income, to determine whether it is more likely than not  that some portion or all of the net deferred tax assets will not be  realized. Based upon the Company&amp;#8217;s recent losses and  uncertainty of future profits, the Company has determined that the  uncertainty regarding the realization of these assets is sufficient  to warrant the need for a full valuation allowance against its U.S.  net deferred tax assets.&lt;/div&gt;    &lt;div style="clear:both; FONT-FAMILY:Times New Roman;FONT-SIZE: 10pt"&gt;&lt;font  size="2"&gt;&amp;#160;&lt;/font&gt;&lt;/div&gt;    &lt;div style="clear:both; FONT-FAMILY:Times New Roman;FONT-SIZE: 10pt;TEXT-ALIGN: justify; MARGIN: 0pt 0px; FONT: 10pt Times New Roman, Times, Serif"&gt;  As a result, the Company has recorded a valuation allowance of  approximately $&lt;font style=" FONT-SIZE: 10pt"&gt;1.7&lt;/font&gt; million as  of September 30, 2012 and an additional valuation allowance of  approximately $&lt;font style=" FONT-SIZE: 10pt"&gt;2.7&lt;/font&gt; million  based upon year to date activity for a total valuation allowance of  approximately $&lt;font style=" FONT-SIZE: 10pt"&gt;4.4&lt;/font&gt; million as  of June 30, 2013.&lt;/div&gt;    &lt;div style="clear:both; FONT-FAMILY:Times New Roman;FONT-SIZE: 10pt"&gt;&lt;font  size="2"&gt;&amp;#160;&lt;/font&gt;&lt;/div&gt;    &lt;div style="clear:both; FONT-FAMILY:Times New Roman;FONT-SIZE: 10pt;TEXT-ALIGN: justify; MARGIN: 0pt 0px; FONT: 10pt Times New Roman, Times, Serif"&gt;  The Company applies the authoritative provisions related to  accounting for uncertainty in income taxes. As required by these  provisions, the Company recognizes the financial statement benefit  of a tax position only after determining that the relevant tax  authority would more-likely-than-not sustain the position following  an audit. For tax positions meeting the more-likely-than-not  threshold, the amount recognized in the financial statements is the  largest benefit that has a greater than 50 percent likelihood of  being reached upon ultimate settlement with the relevant tax  authority. As of June 30, 2013 and September 30, 2012, the Company  has no liabilities recorded for uncertain tax positions. Interest  and penalty charges, if any, related to uncertain tax positions  would be classified as income tax expense in the accompanying  consolidated statement of operations. As of June 30, 2013 and  September 30, 2012, the Company had no accrued interest or  penalties related to uncertain tax positions. The Company currently  has no federal or state tax examinations in progress.&lt;/div&gt;    &lt;div style="clear:both; FONT-FAMILY:Times New Roman;FONT-SIZE: 10pt"&gt;&lt;font  size="2"&gt;&amp;#160;&lt;/font&gt;&lt;/div&gt;    &lt;div style="clear:both; FONT-FAMILY:Times New Roman;FONT-SIZE: 10pt;TEXT-ALIGN: justify; MARGIN: 0pt 0px; FONT: 10pt Times New Roman, Times, Serif"&gt;  The effective rate of (&lt;font style=" FONT-SIZE: 10pt"&gt;8.07&lt;/font&gt;%)  and (&lt;font style=" FONT-SIZE: 10pt"&gt;2.61&lt;/font&gt;%) for the three and  nine months ended June 30, 2013 differs from the U.S. federal  statutory income tax rate of &lt;font style=" FONT-SIZE: 10pt"&gt;  34&lt;/font&gt;% primarily due to a full valuation allowance against the  Company&amp;#8217;s U.S. deferred tax asset. The effective rate of  (&lt;font style=" FONT-SIZE: 10pt"&gt;70.69&lt;/font&gt;%) and (&lt;font style=" FONT-SIZE: 10pt"&gt;72.04&lt;/font&gt;%) for the three and nine months  ended June 30, 2012 is primarily due to the recognition of research  credits.&lt;/div&gt;    &lt;div style="clear:both; FONT-FAMILY:Times New Roman;FONT-SIZE: 10pt"&gt;&lt;font  size="2"&gt;&amp;#160;&lt;/font&gt;&lt;/div&gt;    &lt;div style="clear:both; FONT-FAMILY:Times New Roman;FONT-SIZE: 10pt;TEXT-ALIGN: justify; MARGIN: 0pt 0px; FONT: 10pt Times New Roman, Times, Serif"&gt;  The Company files its tax returns as prescribed by the tax laws of  the jurisdictions in which it operates. The Company&amp;#8217;s tax  filings for federal and state jurisdictions for the tax years  beginning with 2009 are still subject to examination.&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 income taxes. Disclosures may include net deferred tax liability or asset recognized in an enterprise's statement of financial position, net change during the year in the total valuation allowance, approximate tax effect of each type of temporary difference and carryforward that gives rise to a significant portion of deferred tax liabilities and deferred tax assets, utilization of a tax carryback, and tax uncertainties information.</ElementDefenition><ElementReferences>Reference 1: http://www.xbrl.org/2003/role/presentationRef

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