Gene flow is thought to impede genetic divergence and speciation by homogenizing genomes. Recent theory and research suggests that strong enough divergent selection can overpower gene flow, leading to islands of divergence. However, there are alternative explanations for these patterns. Independent evidence that islands of divergence are due to divergent selection would allow these explanations to be distinguished, but such evidence is scarce. Here we present multiple lines of evidence that islands of divergence in a pair of sister morning glory species, Ipomoea cordatotriloba and I. lacunosa, are the outcome of divergent selection in the face of gene flow. We analyzed a SNP dataset across the genome to assess the amount of gene flow, resistance to introgression, and patterns of selection on genes resistant to introgression. We show that differentiation between the two species is much lower in sympatry than in allopatry, consistent with gene flow between the species in sympatry. In addition, highly differentiated SNPs were subject to divergent selection. Finally, despite gene flow in sympatry, SNPs that are highly differentiated in allopatry are resistant to homogenization in sympatry. Our investigation reveals the complex interplay between selection and gene flow that can occur during the early stages of speciation.