Endozoicomonas euniceicola EF212T and Endozoicomonas gorgoniicola PS125T were isolated from soft corals (Eunicea fusca and Plexaura sp., respectively) and sequenced using a PacBio Sequel IIe sequencer. This is the first report of the genome sequences of culturable octocoral-isolated Endozoicomonas strains.