Some groups of marine heterobranch sea slugs (formerly Opisthobranchia) have few discrete characters or hard parts and many ‘cosmopolitan’ species, suggesting an overly conservative taxonomy in need of integrative approaches. Many herbivorous sea slugs in the clade Sacoglossa retain algal chloroplasts that remain functionally photosynthetic for 1–2 weeks, but at least four species can sustain chloroplasts for several months. To better understand the origins of long-term kleptoplasty, we performed an integrative study of the highly photosynthetic species Elysia timida from the Mediterranean and Caribbean populations that were described as E. cornigera but later synonymised with E. timida. Nominal E. cornigera were distinct in their anatomy and aspects of larval development, and had dramatically reduced chloroplast retention compared with E. timida. Mean divergence at three genetic loci was determined for ten pairs of sister species in the genus Elysia, confirming that E. cornigera and E. timida have species level differences. Both taxa had a high degree of population genetic subdivision, but among-population genetic distances were far less than interspecific divergence. In an integrative taxonomic framework, E. cornigera is thus restored to species rank and fully redescribed, and baseline molecular data are presented for evaluating species level differences in the Sacoglossa.