Note that Hotten's list does not include all ships.  

REGISTER OF THE NAMES OF ALL THE PASSENGERS FROM
LONDON DURING ONE WHOLE YEAR, ENDING CHRISTMAS,
1635:

Ship  BONAVENTURE        J Ricrofte, Master 
Ship  BONAVENTURE        J Romsey, Master  
Ship  HOPEWELL           I Wood, Master  
Ship  CHRISTIAN          J White, Master  
Ship  PLANTER            N Trarice,Master 
Ship  PETER BONAVENTURE  I Harman, Master 
Ship  HOPEWELL           W Bundocke, Master 
Ship  ELIZABETH          W Stagg, Master 
Ship  REBECCA            Hodges, Master  
Ship  PAUL               Acklin, Master 
Ship  ELIZA & ANN        R Cowper[or Cooper], Master  
Ship  ENCREASE           R Lea, Master 
Ship  SUSAN & ELLEN      E Payne, Master 
Ship  FALCON             T Irish, Master  
Ship  EXPECTATION        C Billinge, Master 
Ship  ANN & ELIZABETH    J Brookhaven, Master  
Ship  ABIGAIL            R Hackwell,Master 
Ship  DEFENCE            E Bostocke, Master  
Ship  BLESSING           J Lester, Master 
Ship  PHILIP             R Morgan, Master 
Ship  AMERICA            W Barker, Master 
Ship  TRANSPORT          E Walker, Master  
Ship  PAUL               L Betts, Master 
Ship  PIED COW           Ashley, Master 
Ship  LOVE               J Young, Master
Ship  ALICE              R Orchard, Master
Ship  HOPEWELL           T Babb, Master  
Ship  ASSURANCE          I Bromwell & IPewsie,Masters 
Ship  MERCHANT'S HOPE    H Weston, Master  
Ship  ELIZABETH          C Browne, Master 
Ship  BACHELOR           T Webb, Master 
Ship  GLOBE              J Blackman, Master  
Ship  SAFETY             J Graunt, Master 
Ship  GEORGE             J Severne, Master 
Ship  THOMAS             H Taverner, Master 
Ship  WILLIAM & JOHN     R Langram, Master  
Ship  DAVID              J Hogg, Master 
Ship  TRUELOVE           J Gibbs, Master 
Ship  DORSET             J Flower, Master
Ship  JOHN               J Waymoth, Master 
Ship  AMITY              G Downes, Master
Ship  CONSTANCE          C Campion, Master 
Ship  ABRAHAM            J Barker, Master 
Ship  EXPEDITION         P Blackley, Master 
Ship  FRIENDSHIP         -----,  Master
 

List of ships conveying emigrants to Virginia before 1625-6


 ABIGAIL               GEORGE                 PHOENIX     
 AMBROSE               GIFT                   PROSPEROUS     
 ANN                   GREAT HOPEWELL         RETURN     
 BLESSING              GOD'S GIFT             SAMPSON     
 BONA NOVA             GOD SPEED              SAMUEL     
 BONAVENTURE           HERCULES               SARAH     
 BONNY BESSIE          HOPEWELL               SEAFLOWER     
 CHARITY               JACOB                  SEAVENTURE     
 CHARLES               JAMES                  SOUTHAMPTON     
 CONCORD               JONATHAN               STAR     
 DELAWARE              JOHN & FRANCIS         SUPPLY     
 DELIVERANCE           LONDON MERCHANT        SUSAN     
 DIANA                 MARGARET               SWALLOW     
 DISCOVERY             MARGARET & JOHN        SWAN     
 DUE RETURN            MARMADUKE              TEMPERANCE     
 DUTY                  MARY ANN MARGARET      TIGER     
 EDWIN                 MARY & JAMES           TREASURER     
 ELIANOR               MARY MARGARET          TRIAL     
 ELIZABETH             MARYGOLD               TRUELOVE     
 FALCON                MARY PROVIDENCE        UNITY     
 FLYING HART           NEPTUNE                WARWICK     
 FRANCIS BONAVENTURE   NOAH                   WILLIAM & JOHN      
 FURTHERANCE           PATIENCE               WILLIAM & THOMAS     
 

RETURNS OF THOSE WHO EMBARKED FROM IPSWICH AND
  WEYMOUTH FOR NEW ENLAND, 1634 TO 1637 
   From Ipswich, in the Ship    FRANCIS ... J.Cuttings,Master
   From Ipswich, in the Ship    ELIZABETH ... W.Andrews,Master
   From Weymouth, in the Ship     -----[1635]...  -----,Master

REGISTER OF PERSONS ABOUT TO PASS INTO FOREIGN
  PARTS, FROM MARCH TO SEPT., 1637     
   From Ipswich, in the       JOHN & DOROTHY ... W.Andrewes,Master 
   From Yarmouth, in the      ROSE          ... W.Andrewes,Junr. Master 
   From Southampton, in the   VIRGIN [1639]..J.Weare & J.Delshay, Masters                                             
   From Southampton, in the   BEVIS [1638] ... R. Batten, Master