Second Supplement Indenture



 Exhibit 4.1 
 SECOND SUPPLEMENTAL INDENTURE 
 (TO CONVERTIBLE INDENTURE) 

THIS SECOND SUPPLEMENTAL INDENTURE (this “Second Supplemental Indenture”) is dated as of May 3, 2012, and
has been entered into by and between Horizon Lines, Inc., a Delaware corporation, having its principal office at 4046 Colony Road, Suite 200, Charlotte, North Carolina 28211 (the “Company”), the guarantors listed on the signature
pages hereto (the “Guarantors”) and U.S. Bank National Association, as trustee (the “Trustee”) and collateral agent. 
 RECITALS 
 WHEREAS, the Company, the Guarantors and the Trustee
previously entered into that certain indenture dated as of October 5, 2011 (as supplemented by that certain first supplemental indenture dated as of April 9, 2012, the “Indenture”), providing for the issuance of the
Company’s 6.00% Series A Convertible Senior Secured Notes due 2017 (the “Series A Notes”) and 6.00% Series B Mandatorily Convertible Senior Secured Notes (the “Series B Notes” and, together with the Series A
Notes, the “Notes”); 
 WHEREAS, Series A Notes in the aggregate principal amount of $178,781,456 and
Series B Notes in the aggregate principal amount of $49,661,522 are currently outstanding under the Indenture; 

WHEREAS, Section 11.01 of the Indenture provides that the Company may increase the Conversion Rate of the Series A Notes
without the consent of the Noteholders; 
 WHEREAS, the Company has been authorized by Board Resolution to enter into
this Second Supplemental Indenture; 
 WHEREAS, the Company desires to amend certain provisions of the Indenture, as set
forth in Article I of this Second Supplemental Indenture; and 
 WHEREAS, all acts and requirements necessary to make
this Second Supplemental Indenture the legal, valid and binding obligation of the Company and the Guarantors have been done. 

AGREEMENT 

NOW, THEREFORE, in consideration of the premises and the covenants and agreements contained herein, and for other good and
valuable consideration the receipt of which is hereby acknowledged, and for the equal and proportionate benefit of the Holders of the Notes, the Company and the Trustee hereby agree as follows: 

ARTICLE I 

AMENDMENTS TO INDENTURE 
 Section 1.01 Amendment to Section 1.01 of the Indenture. The definition of Series A Conversion Rate in Section 1.01 of the Indenture is hereby amended and restated in
its entirety to read as follows: 
 “Series A Conversion Rate” means 402.3272 shares of Common
Stock per $1,000 principal amount of Series A Notes, subject to adjustment as set forth herein. 
 ARTICLE II 

MISCELLANEOUS 
 Section 2.01 Instruments To Be Read Together. This Second Supplemental Indenture is executed as and shall constitute an indenture supplemental to and in implementation of the Indenture, and
the Indenture and this Second Supplemental Indenture shall henceforth be read together. This Second Supplemental Indenture shall form a part of the Indenture for all purposes, and every Holder of Notes shall be bound hereby and thereby. 







 Section 2.02 Confirmation. The Indenture as amended and supplemented by this
Second Supplemental Indenture is in all respects confirmed and preserved. 
 Section 2.03 Terms Defined. Capitalized
terms used in this Second Supplemental Indenture and not otherwise defined herein shall have the meanings assigned to such terms in the Indenture. 
 Section 2.04 Trust Indenture Act Controls. If any provision of this Second Supplemental Indenture limits, qualifies or conflicts with another provision that is required to be included in this
Second Supplemental Indenture or the Indenture by the Trust Indenture Act of 1939, as amended, as in force at the date that this Second Supplemental Indenture is executed, the provisions required by the Trust Indenture Act of 1939 shall control.

 Section 2.05 Headings. The headings of the Articles and Sections of this Second Supplemental Indenture have been
inserted for convenience of reference only, and are not to be considered a part hereof and shall in no way modify or restrict any of the terms and provisions hereof. 
 Section 2.06 Governing Law. The internal law of the State of New York shall govern this Second Supplemental Indenture without giving effect to applicable principles of conflicts of law to the
extent that the application of the laws of another jurisdiction would be required thereby. 
 Section 2.07
Counterparts. This Second Supplemental Indenture may be executed in any number of counterparts, each of which so executed shall be deemed to be an original, but all such counterparts shall together constitute but one and the same instrument.

 Section 2.08 Effectiveness; Termination. The provisions of this Second Supplemental Indenture will become
effective immediately upon its execution by the Trustee in accordance with the provisions of Section 11.03 of the Indenture; provided, that the amendments to the Indenture set forth in Section 1.01 of this Second Supplemental Indenture
shall become operative as specified in Section 1.01 hereof. 
 Section 2.09 Acceptance by Trustee. The Trustee
accepts the amendments to the Indenture effected by this Second Supplemental Indenture and agrees to execute the trusts created by the Indenture as hereby amended, but only upon the terms and conditions set forth in the Indenture. 

Section 2.10 Responsibility of Trustee. The recitals contained herein shall be taken as the statements of the Company, and
the Trustee assumes no responsibility for their correctness. The Trustee makes no representations as to the validity or sufficiency of this Second Supplemental Indenture. 

  
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 IN WITNESS WHEREOF, the parties hereto have caused this Second Supplemental Indenture
to be duly executed, all as of the date first written above. 
  

			
	HORIZON LINES, INC.
		
	By:	 	  

		
	Name:	 	Michael F. Zendan II
	Title:	 	Senior Vice President, General Counsel and Secretary
	
	HORIZON LINES, LLC
	 HORIZON LINES HOLDING CORP.
 HAWAII STEVEDORES, INC.

	HORIZON LINES OF PUERTO RICO, INC.
	 HORIZON LINES OF ALASKA, LLC
 HORIZON LINES OF GUAM, LLC
 HORIZON LINES VESSELS, LLC

	H-L DISTRIBUTION SERVICE, LLC
	HORIZON LOGISTICS, LLC
	 AERO LOGISTICS, LLC

SEA-LOGIX, LLC
 HORIZON SERVICES GROUP,
LLC

		
	By:	 	  

		
	Name:	 	Michael F. Zendan II
	Title:	 	Secretary


 [Signature Page to Second Supplemental Indenture (Convertible Indenture)] 







 
			
	U.S. BANK NATIONAL ASSOCIATION,
	as Trustee and Collateral Agent
		
	By:	 	  

		
	Name:	 	  

		
	Title:	 	  



 [Signature Page to Second Supplemental Indenture (Convertible Indenture)]