Species of the genus Elysia Risso, 1818 have relatively few external characters useful for species identification, and features such as papillae and/or color markings on the body surface are often used to classify and identify species. Elysia atroviridis Baba, 1955 and E. setoensis Hamatani, 1968, for example, have been described as distinct based mainly on such characters. Close examinations of 46 specimens identifiable as either species collected from nine localities in Japan revealed that many specimens exhibited mixed features of the two species. Detailed comparisons of radular morphology could also not differentiate the two species. With phylogenetic analyses based on COI and 16S rRNA (1072 bp in total), all of the examined specimens formed a single clade with very little variation among specimens. The AMOVA of the specimen haplotypes showed there was no significant genetic differentiation in relation to differences in external morphology, geographic region, or algal host. Our results indicate that E. atroviridis and E. setoensis are conspecific. In contrast, cryptic species were found in two other clades of congeners, indicating that further taxonomic scrutiny is needed within the genus.