Speciation is a direct consequence of isolated populations in taxa with low dispersal potential. The brooding crustacean Excirolana braziliensis, with a presumably wide geographic range of distribution (~16° N-41° S in the Pacific and ~19° N-35° S in the Atlantic), has been detected to correspond to cryptic species on the coast of Panama. Latitudinal variations in reproductive features in E. braziliensis have been attributed to phenotypic plasticity, however, the differences may be the result of divergent populations. Considering that the taxon has been reported to be a complex of cryptic species in other geographic areas and given the phenotypic differences detected along its distribution range, we hypothesized that E. braziliensis is a complex of species in the coast of Chile. We used partial cytochrome c oxidase subunit I (COI) sequences from 132 individuals with the diagnostic morphology of E. braziliensis collected along ~2200 km of coast to determine the genetic structure of E. braziliensis. Phylogenetic and phylogeographic analyses showed three distinct clades with 14 to 19 % of genetic divergence and high values of genetic differentiation. Intra and inter-clade divergence revealed the existence of a species complex of E. braziliensis on the coast of Chile, supporting growing evidence of the high abundance of cryptic species in marine invertebrate taxa.