Biogeographic barriers can set range limits for marine organisms by restricting migration, or because subsequent recruitment may be prevented by post-settlement selection. We used microsatellite and mtDNA data for adults and juveniles of the barnacle Catomerus polymerus to test the hypothesis that persistent differentiation of populations occurring to the northeast as compared with south and west of the southeast Australian biogeographic barrier (SEABB) is maintained by selection rather than dispersal limitation. We also explored the dispersal of C. polymerus along uninterrupted linear stretches of coastline (1440 km) to the east and west (120 km) of the SEABB. Within the regions flanking the SEABB, we found little genetic differentiation (FST < 0.006), implying strong gene flow. In contrast, adults to the northeast were significantly differentiated from those to the south and southwest of the SEABB (FST = 0.10), confirming some restriction of gene flow by the SEABB. Similarly, Bayesian analyses revealed eastern and western clusters of adults and juveniles, with the great majority assigning strongly to their region of collection. Nevertheless, 5 of 556 adults, and 10 of 537 juveniles, had genotypes that aligned more strongly with the genetic cluster of the opposite side of the SEABB, implying that migration does occur. Mitochondrial DNA sequence data (n = 71) revealed one additional eastern adult with an immigrant western haplotype. Our data imply that differentiation of eastern and western lineages reflects both restricted dispersal and possibly regional-scale selection acting on immigrant genotypes.