Exhibit 32.1

HORIZON LINES, INC.

CERTIFICATION PURSUANT TO 18 U.S.C. SECTION 1350, AS ADOPTED PURSUANT TO

SECTION 906 OF THE SARBANES-OXLEY ACT OF 2002

In connection with the Annual Report of Horizon Lines, Inc. (the “Company”) on Form 10-K for the period ending December 26, 2010 as filed with the Securities and Exchange Commission on the date hereof (the “Report”), I, Stephen H. Fraser, President and Chief Executive Officer of the Company, certify, pursuant to 18 U.S.C. § 1350, as adopted pursuant to § 906 of the Sarbanes-Oxley Act of 2002, that:

(1) The Report fully complies with the requirements of Section 13(a) or 15(d) of the Securities Exchange Act of 1934; and

(2) The information contained in the Report fairly presents, in all material respects, the financial condition and results of operations of the Company.

/s/  STEPHEN H. FRASER

Stephen H. Fraser

President and Chief Executive Officer

(Principal Executive Officer)

March 28, 2011