Nearly 13% of opisthobranch gastropods in the Atlantic Ocean are regarded as amphi-Atlantic (i.e. species occurring on both eastern and western coastlines of the Atlantic realm). This assumption has been broadly based on morpho-anatomical similarities and has rarely been tested within a molecular phylogenetic framework. Among opisthobranchs, the order Sacoglossa is renowned for its difficult and confusing species taxonomy, particularly in some genera like Elysia, where several cases of cryptic speciation have been documented. Moreover, the width of the Atlantic realm poses a serious challenge to the idea of trans-Atlantic dispersal, particularly in nonplanktotrophic species. The species Bosellia mimetica, Elysia timida and Thuridilla picta are three sacoglossan opisthobranchs with amphiAtlantic status, but doubts have been raised about the conspecificity of eastern and western populations. Here we used methods to test molecular phylogenetic whether the Atlantic Ocean constitutes a barrier for dispersal and hence whether eastern and western populations belong to the same species. We used the criteria of divergence and reciprocal monophyly, supported by concordant genealogically independent genetic markers, to define species. Maximum-likelihood and Bayesian analyses of partial DNA sequences of the mitochondrial cytochrome c oxidase subunit I and 16S rRNA genes and nuclear gene Histone-3 (H3) were used to produce phylogenetic trees. We conclude that the eastern Atlantic species B. mimetica is not amphi-Atlantic, although the H3 gene did not recover reciprocal monophyly between western and eastern populations, perhaps in a result of incomplete lineage-sorting. Elysia timida is the only species showing an amphi-Atlantic distribution, but possibly due to recent introduction in the tropical western Atlantic. Thuridilla picta is restricted to the western Atlantic and therefore not amphi-Atlantic. Populations of ‘T. picta’ inhabiting the Macaronesian archipelagos of Azores and Madeira are a colour form of the eastern Atlantic T. hopei. Our results highlight the difficulty surrounding systematics of Sacoglossa sea slugs and provide further evidence that cryptic speciation is common in the group.