Intraspecific clinal systems are ideal for investigating the how divergence occurs in the presence of gene flow because they represent a balance between selection and gene flow prior to speciation. High dispersal marine species with clinal variation are particularly informative to test for divergent selection because selection likely is strong enough to counteract high gene flow. The degree of population structure varies considerably among loci, such that the genome acts as a sieve allowing gene flow at neutral loci and impeding it at selected loci, creating a genomic mosaic of differentiation. In this study, I examine genomic and geographic patterns of differentiation among parapatric populations of the eastern oyster (Crassostrea virginica) along their contact zone in Florida estuaries. The planktotrophic larval phase of this species gives it the potential for regular long-distance dispersal and genetically homogeneous populations. However Florida populations at the center of its range exhibit a sharp step cline at some loci, suggesting a role for divergent selection. Using 217 AFLP loci, including seven candidate loci for differential selection between the two populations, I genotyped 1,011 spat over two seasons and 274 adults at sites along the contact zone. I examined: (1) whether genome scans can detect divergent selection in a clinal system, (2) the genomic and geographic patterns of differentiation along the cline at neutral and selected loci, and (3) regional patterns of differentiation and genotypic distributions among the life stages. Results demonstrated: (1) candidate loci for regionally divergent selection, (2) a genomic and geographic mosaic of differentiation, (3) regional and localized selection at a non-trivial portion of loci, (4) lower recruitment and some mortality in the center of the cline, and (5) strong exogenous, post-settlement viability selection against intermediate and non-native-like genotypes. While a combination of neutral and adaptive processes likely shape genomic and geographic patterns of differentiation, this study revealed evidence for divergent selection in an estuarine species with high potential for gene flow. Overall, these results point to a major role for post-zygotic, environment-dependent selection in the maintenance of the contact zone between Atlantic and Gulf-type oyster populations.