Genetic variation at 10 enzyme loci was analysed in Elysia timida sacoglossan mollusc samples, originating from both coastal lagoon and marine sites. The observed heterozygosity ranged from 0.390 (Los Urrutias) to 0.277 (Tabarca). Marine and coastal lagoon populations were characterised by exclusive alleles. Examination of the spatial structure was performed using Nei’s distances and F-statistics, and indicated significant genetic differences between marine groups and coastal lagoon populations. Multivariate analysis of allele frequencies also suggested that different arrays of genotypes prevail in coastal lagoon samples compared to marine ones.