Divergent selection in the face of gene flow is usually associated with a heterogeneous genomic landscape of divergence in nascent species pairs. However, multiple factors, such as divergent selection and local recombination rate variation, can influence the formation of these genomic island. This conundrum can be solved through examination of the genomic landscapes of species pairs that are still in the early stages of evolution. In this study, population genomics analyses were undertaken using a wide range of sampling and whole-genome resequencing data from 96 unrelated individuals of Kentish plover (Charadrius alexandrinus) and white-faced plover (C. dealbatus). We suggest that the two species exhibit varying levels of population admixture along the Chinese coast and on Taiwan Island. Genome-wide analyses for introgression indicate that ancient introgression had occurred in Taiwan population, and recurrent gene flow is still ongoing in mainland coastal populations. Furthermore, we identified a few genomic regions with significant levels of interspecific differentiation and local recombination suppression, which contain several genes potentially associated with disease resistance, coloration, and regulation of plumage moulting, thus may be connected to the phenotypic and ecological divergence of the two nascent species. Overall, our findings suggest that divergent selection in low recombination regions may be the main force in shaping the genomic islands in two incipient shorebird species.