Acute hepatopancreatic necrosis disease (AHPND), also known as early mortality syndrome (EMS), causes high mortalities in cultured shrimps in Asia (L. Tran et al., Dis. Aquat. Organ. 105:45-55, 2013, http://dx.doi.org/10.3354/dao02621). Here, we report the draft genome sequence of one Mexican strain of Vibrio parahaemolyticus that causes similar clinical signs in diseased shrimps.