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Background  There is a biogeographic break located at 30°S in the southeast Pacific, in a coastal area of strong environmental discontinuities. Several marine benthic taxa with restricted dispersal have a coincident phylogeographic break at 30°S, indicating that genetic structure is moulded by life history traits that limit gene flow and thereby promote divergence and speciation. In order to evaluate intraspecific divergence at this biogeographic break, we investigated the genetic and morphological variation of the directly developing beach isopod  Excirolana hirsuticauda  along 1900 km of the southeast Pacific coast, across 30°S.    Results  The  COI  sequences and microsatellite data both identified a strong discontinuity between populations of  E. hirsuticauda  to the north and south of 30°S, and a second weaker phylogeographic break at approximately 35°S. The three genetic groups were evidenced by different past demographic and genetic diversity signatures, and were also clearly distinguished with microsatellite data clustering. The  COI  sequences established that the genetic divergence of  E. hirsuticauda  at 30°S started earlier than divergence at 35°. Additionally, the three groups have different past demographic signatures, with probable demographic expansion occurring earlier in the southern group (south of 35°S), associated with Pleistocene interglacial periods. Interestingly, body length, multivariate morphometric analyses, and the morphology of a fertilization-related morphological character in males, the  appendix masculina , reinforced the three genetic groups detected with genetic data.    Conclusions  The degree of divergence of  COI  sequences, microsatellite data, and morphology was concordant and showed two geographic areas in which divergence was promoted at differing historical periods. Variation in the  appendix masculina  of males has probably promoted reproductive isolation. This variation together with gene flow restrictions promoted by life history traits, small body size, oceanographic discontinuities and sandy-beach habitat continuity, likely influenced species divergence at 30°S in the southeast Pacific coast. The degree of genetic and morphological differentiation of populations to the north and south of 30°S suggests that  E. hirsuticauda  harbours intraspecific divergence consistent with reproductive isolation and an advanced stage of speciation. The speciation process within  E. hirsuticauda  has been shaped by both restrictions to gene flow and a prezygotic reproductive barrier.    Electronic supplementary material  The online version of this article (10.1186/s12862-019-1442-z) contains supplementary material, which is available to authorized users.

Genetic and morphological divergence at a biogeographic break in the beach-dwelling brooder Excirolana hirsuticauda Menzies (Crustacea, Peracarida)