Document:

EX-4.1

 Exhibit 4.1 

FIRST SUPPLEMENTAL INDENTURE (this “First Supplemental Indenture”), dated as of January 8, 2014, among Navios Maritime
Acquisition Corporation, a Marshall Islands corporation, (the “Company”), Navios Acquisition Finance (US) Inc., a Delaware corporation (together with the Company, the “Co-Issuers”), and Lefkada Shipping Corporation,
Kerkyra Shipping Corporation, and Zakynthos Shipping Corporation, (each a “Guaranteeing Subsidiary”), each a Marshall Islands corporation and an indirect subsidiary of the Company, the other Guarantors (as defined in the Indenture
referred to herein) and Wells Fargo Bank, National Association, as trustee (or its permitted successor) under the Indenture referred to below (the “Trustee”) and as collateral trustee (or its permitted successor) under the Indenture
referred to below (the “Collateral Trustee”). 
 WITNESSETH 

WHEREAS, the Co-Issuers and the Guarantors have heretofore executed and delivered to the Trustee an indenture (the
“Indenture”), dated as of November 13, 2013 providing for the issuance of 8.125% First Priority Ship Mortgage Notes due 2021 (the “Notes”); 

WHEREAS, the Indenture provides that under certain circumstances each Guaranteeing Subsidiary shall execute and deliver to the Trustee a
supplemental indenture pursuant to which each Guaranteeing Subsidiary shall unconditionally guarantee all of the Co-Issuers’ obligations under the Notes and the Indenture on the terms and conditions set forth herein (the “Note
Guarantee”); and 
 WHEREAS, pursuant to Section 9.01 of the Indenture, the Trustee is authorized to execute and deliver this
First Supplemental Indenture. 
 NOW, THEREFORE, in consideration of the foregoing and for other good and valuable consideration, the
receipt of which is hereby acknowledged, each Guaranteeing Subsidiary and the Trustee mutually covenant and agree for the equal and ratable benefit of the Holders of the Notes as follows: 

1. CAPITALIZED TERMS. Capitalized terms used herein without definition shall have the meanings assigned to them in the Indenture. 

2. AGREEMENT TO GUARANTEE. Each Guaranteeing Subsidiary hereby agrees to provide an unconditional Guarantee, on and subject to the terms,
conditions and limitations set forth in the Notation of Guarantee and in the Indenture, including, but not limited, to Article Ten thereof. 

4. NEW YORK LAW TO GOVERN. THIS FIRST SUPPLEMENTAL INDENTURE SHALL BE GOVERNED BY AND CONSTRUED IN ACCORDANCE WITH THE LAWS OF THE STATE OF
NEW YORK, WITHOUT GIVING EFFECT TO CONFLICTS OF LAW PRINCIPLES TO THE EXTENT THAT THE APPLICATION OF THE LAWS OF ANOTHER JURISDICTION WOULD BE REQUIRED THEREBY. 

 5. COUNTERPARTS. The parties may sign any number of copies of this First Supplemental Indenture.
Each signed copy shall be an original, but all of them together represent the same agreement. 
 6. EFFECT OF HEADINGS. The Section headings
herein are for convenience only and shall not affect the construction hereof. 
 7. THE TRUSTEE. The Trustee shall not be responsible in any
manner whatsoever for or in respect of the validity or sufficiency of this First Supplemental Indenture or for or in respect of the recitals contained herein, all of which recitals are made solely by each Guaranteeing Subsidiary and the Co-Issuers.

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

					
	LEFKADA SHIPPING CORPORATION
	KERKYRA SHIPPING CORPORATION
	ZAKYNTHOS SHIPPING CORPORATION
			
		 	By:	 	 /s/ Anna Kalathakis

		 		 	Name:   Anna Kalathakis
		 		 	Title:     Treasurer/Director
	
	 NAVIOS MARITIME ACQUISITION
        CORPORATION

			
		 	By:	 	 /s/ Vasiliki Papaefthymiou

		 		 	Name:   Vasiliki Papaefthymiou
		 		 	Title:     Secretary
	
	 NAVIOS ACQUISITION FINANCE (US) INC.

			
		 	By:	 	 /s/ Vasiliki Papaefthymiou

		 		 	Name:   Vasiliki Papaefthymiou
		 		 	Title:     President/Secretary
	
	DONOUSSA SHIPPING CORPORATION
	SCHINOUSA SHIPPING CORPORATION
	SIKINOS SHIPPING CORPORATION
	LIMNOS SHIPPING CORPORATION
	SKYROS SHIPPING CORPORATION
	ALONNISOS SHIPPING CORPORATION
	MAKRONISOS SHIPPING CORPORATION
	IRAKLIA SHIPPING CORPORATION
	THASOS SHIPPING CORPORATION
	SAMOTHRACE SHIPPING CORPORATION
	PAXOS SHIPPING CORPORATION
	ANTIPAXOS SHIPPING CORPORATION
	OINOUSSES SHIPPING CORPORATION
	ANTIPSARA SHIPPING CORPORATION
	PSARA SHIPPING CORPORATION

					
	KITHIRA SHIPPING CORPORATION
	ANTIKITHIRA SHIPPING CORPORATION
	AMINDRA NAVIGATION CO.
	SERIFOS SHIPPING CORPORATION
	FOLEGANDROS SHIPPING CORPORATION
			
		 	By:	 	 /s/ Anna Kalathakis

		 		 	Name:   Anna Kalathakis
		 		 	Title:     Treasurer/Director
	
	SHINYO DREAM LIMITED
	SHINYO KANNIKA LIMITED
	SHINYO LOYALTY LIMITED
	SHINYO NAVIGATOR LIMITED
	SHINYO OCEAN LIMITED
	SHINYO SAOWALAK LIMITED
	SHINYO KIERAN LIMITED
			
		 	By:	 	 /s/ Alexandros Laios

		 		 	Name:   Alexandros Laios
		 		 	Title:     Director
	
	AEGEAN SEA MARITIME HOLDINGS INC.
	THERA SHIPPING CORPORATIONTINOS SHIPPING CORPORATION
	AMORGOS SHIPPING CORPORATION
	ANDROS SHIPPING CORPORATION
	ANTIPAROS SHIPPING CORPORATION
	CRETE SHIPPING CORPORATION
	IKARIA SHIPPING CORPORATION
	IOS SHIPPING CORPORATION
	KOS SHIPPING CORPORATION
	MYTILENE SHIPPING CORPORATION
	RHODES SHIPPING CORPORATION
	SIFNOS SHIPPING CORPORATION
	SKIATHOS SHIPPING CORPORATION
	SKOPELOS SHIPPING CORPORATION
	SYROS SHIPPING CORPORATION
			
		 	By:	 	 /s/ George Achniotis

		 		 	Name:   George Achniotis
		 		 	Title:     President/ Director

 
					
	 WELLS FARGO BANK, NATIONAL
                ASSOCIATION,
                as Trustee

			
		 	By:	 	 /s/ Martin Reed

		 		 	Name:   Martin Reed
		 		 	Title:     Vice President
	
	 WELLS FARGO BANK, NATIONAL
                ASSOCIATION,
                as Collateral Trustee

			
		 	By:	 	 /s/ Martin Reed

		 		 	Name:   Martin Reed
		 		 	Title:     Vice PresidentEX-4.2

 Exhibit 4.2 

SECOND SUPPLEMENTAL INDENTURE (this “Second Supplemental Indenture”), dated as of February 20, 2014, among Navios
Maritime Acquisition Corporation, a Marshall Islands corporation, (the “Company”), Navios Acquisition Finance (US) Inc., a Delaware corporation (together with the Company, the “Co-Issuers”), and Navios Acquisition
Europe Finance Inc. (the “Guaranteeing Subsidiary”), a Marshall Islands corporation and a direct subsidiary of the Company, the other Guarantors (as defined in the Indenture referred to herein) and Wells Fargo Bank, National
Association, as trustee (or its permitted successor) under the Indenture referred to below (the “Trustee”) and as collateral trustee (or its permitted successor) under the Indenture referred to below (the “Collateral
Trustee”). 
 WITNESSETH 

WHEREAS, the Co-Issuers and the Guarantors have heretofore executed and delivered to the Trustee an indenture (the
“Indenture”), dated as of November 13, 2013 providing for the issuance of 8.125% First Priority Ship Mortgage Notes due 2021 (the “Notes”); 

WHEREAS, the Indenture provides that under certain circumstances each Guaranteeing Subsidiary shall execute and deliver to the Trustee a
supplemental indenture pursuant to which a Guaranteeing Subsidiary shall unconditionally guarantee all of the Co-Issuers’ obligations under the Notes and the Indenture on the terms and conditions set forth herein (the “Note
Guarantee”); and 
 WHEREAS, pursuant to Section 9.01 of the Indenture, the Trustee is authorized to execute and deliver this
Second Supplemental Indenture. 
 NOW, THEREFORE, in consideration of the foregoing and for other good and valuable consideration, the
receipt of which is hereby acknowledged, the Co-Issuers, the Guaranteeing Subsidiary and the Trustee mutually covenant and agree for the equal and ratable benefit of the Holders of the Notes as follows: 

1. CAPITALIZED TERMS. Capitalized terms used herein without definition shall have the meanings assigned to them in the Indenture. 

2. AGREEMENT TO GUARANTEE. The Guaranteeing Subsidiary hereby agrees to provide an unconditional Guarantee, on and subject to the terms,
conditions and limitations set forth in the Notation of Guarantee and in the Indenture, including, but not limited, to Article Ten thereof. 

4. NEW YORK LAW TO GOVERN. THIS SECOND SUPPLEMENTAL INDENTURE SHALL BE GOVERNED BY AND CONSTRUED IN ACCORDANCE WITH THE LAWS OF THE STATE OF
NEW YORK, WITHOUT GIVING EFFECT TO CONFLICTS OF LAW PRINCIPLES TO THE EXTENT THAT THE APPLICATION OF THE LAWS OF ANOTHER JURISDICTION WOULD BE REQUIRED THEREBY. 

5. COUNTERPARTS. The parties may sign any number of copies of this Second Supplemental Indenture. Each signed copy shall be an original, but
all of them together represent the same agreement. 

 6. EFFECT OF HEADINGS. The Section headings herein are for convenience only and shall not affect
the construction hereof. 
 7. THE TRUSTEE. The Trustee shall not be responsible in any manner whatsoever for or in respect of the validity
or sufficiency of this Second Supplemental Indenture or for or in respect of the recitals contained herein, all of which recitals are made solely by the Guaranteeing Subsidiary and the Co-Issuers. 

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

			
	NAVIOS ACQUISITION EUROPE FINANCE INC.,
	as guarantor
		
	By:	 	 /s/ Alexandros Laios

		 	Name:   Alexandros Laios
		 	Title:     Secretary /Director
	
	NAVIOS MARITIME ACQUISITION CORPORATION
		
	By:	 	 /s/ Anna Kalathaki

		 	Name:   Anna Kalathaki
		 	Title:     Director
	
	NAVIOS ACQUISITION FINANCE (US) INC.
		
	By:	 	 /s/ Vasiliki Papaefthymiou

		 	Name:   Vasiliki Papaefthymiou
		 	Title:     Director
	
	LEFKADA SHIPPING CORPORATION
	KERKYRA SHIPPING CORPORATION
	ZAKYNTHOS SHIPPING CORPORATION
	DONOUSSA SHIPPING CORPORATION
	SCHINOUSA SHIPPING CORPORATION
	SIKINOS SHIPPING CORPORATION
	LIMNOS SHIPPING CORPORATION
	SKYROS SHIPPING CORPORATION
	ALONNISOS SHIPPING CORPORATION
	MAKRONISOS SHIPPING CORPORATION
	IRAKLIA SHIPPING CORPORATION
	THASOS SHIPPING CORPORATION
	SAMOTHRACE SHIPPING CORPORATION
	PAXOS SHIPPING CORPORATION
	ANTIPAXOS SHIPPING CORPORATION
	OINOUSSES SHIPPING CORPORATION
	ANTIPSARA SHIPPING CORPORATION
	PSARA SHIPPING CORPORATION
	KITHIRA SHIPPING CORPORATION
	ANTIKITHIRA SHIPPING CORPORATION
	AMINDRA NAVIGATION CO.
	SERIFOS SHIPPING CORPORATION
	 FOLEGANDROS SHIPPING CORPORATION,

as guarantors

		
	By:	 	 /s/ Alexandros Laios

		 	Name:   Alexandros Laios
		 	Title:     Director

 
			
	SHINYO DREAM LIMITED
	SHINYO KANNIKA LIMITED
	SHINYO LOYALTY LIMITED
	SHINYO NAVIGATOR LIMITED
	SHINYO OCEAN LIMITED
	 SHINYO SAOWALAK LIMITED,
 as
guarantors

		
	By:	 	 /s/ Alexandros Laios

		 	Name:   Alexandros Laios
		 	Title:     Director
	
	AEGEAN SEA MARITIME HOLDINGS INC.
	THERA SHIPPING CORPORATION
	TINOS SHIPPING CORPORATION
	AMORGOS SHIPPING CORPORATION
	ANDROS SHIPPING CORPORATION
	ANTIPAROS SHIPPING CORPORATION
	CRETE SHIPPING CORPORATION
	IKARIA SHIPPING CORPORATION
	IOS SHIPPING CORPORATION
	KOS SHIPPING CORPORATION
	MYTILENE SHIPPING CORPORATION
	RHODES SHIPPING CORPORATION
	SIFNOS SHIPPING CORPORATION
	SKIATHOS SHIPPING CORPORATION
	SKOPELOS SHIPPING CORPORATION
	 SYROS SHIPPING CORPORATION,
 as
guarantors

		
	By:	 	 /s/ Anna Kalathaki

		 	Name:   Anna Kalathaki
		 	Title:     Director

 [Signature Page to Second Supplemental Indenture] 

			
	SHINYO KIERAN LIMITED
		
	By:	 	 /s/ Leonidas Korres

		 	Name:   Leonidas Korres
		 	Title:     Director

 [Signature Page to Second Supplemental Indenture] 

			
	WELLS FARGO BANK, NATIONAL
		 	 ASSOCIATION,

as Trustee

		
	By:	 	 /s/ Martin Reed

		 	Name:   Martin Reed
		 	Title:     Vice President
	
	WELLS FARGO BANK, NATIONAL
		 	 ASSOCIATION,

as Collateral Trustee

		
	By:	 	 /s/ Martin Reed

		 	Name:   Martin Reed
		 	Title:     Vice President

 [Signature Page to Second Supplemental Indenture]

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