Ecological or reproductive barriers can maintain species by preventing introgression in closely related taxa when their distributions overlap. In sympatry, sister-taxa may have greater genetic divergence than comparing the sister-taxa in allopatric parts of their range. When analyzing populations within a species, this may translate to greater genetic divergence between sympatry and allopatry. This genetic differentiation can be caused by either genetic drift or natural selection, depending on the evolutionary history of secondary contact. To identify a selective process, it is critical to find genes responsible for maintaining species barriers in sympatry. Here, we examined the role of natural selection in genetic differentiation within two recently diverged rockfish species, Sebastes diaconus and Sebastes mystinus. These species overlap along over 400 km of coastline in the eastern Pacific, with no evidence of hybridization. We found evidence of geographic genetic differentiation across a large span of the S. diaconus range, but not within S. mystinus. For both species, we identified outlier loci associated with regions of the genome under directional selection in allopatric versus sympatric populations. We also found signals of directional selection in shared genomic regions of both species, suggesting the evolutionary process of reinforcement maintained species boundaries once the two species were in secondary contact.