Several authors have synonymised
Elysia margaritae with other species of
Elysia. Thompson and Jaklin (1988) considered it as a junior synonym of
Elysia timida, without any justification, whereas Bouchet (1984) considered it a junior synonym of
E. viridis, also providing no arguments. However, Ortea et al. (1998), discussing Canary Islands
E. timida specimens, considered
E. margaritae a valid species; moreover, they proposed that
Elysia gordanae should be considered a junior synonym. Regarding the latter statement, we have to point out that
E. gordanae has a serrated edge to its radular teeth, and rounded edges of the parapodia, with small white protuberances, which have not been mentioned for
E. margaritae. This leads us to consider both species to be different. Our conclusion is that
E. margaritae is a valid species, because of its unique colour pattern, large size, and smooth radular teeth. Nevertheless, the lack of additional specimens with this morphology collected since its original description in 1962, even though the eastern Iberian coasts have been intensively studied over the last three decades by several authors, and the lack of data about the size of the radular teeth, suggests that some doubts about its true taxonomic identity still exist.