The molecular basis of the incipient stage of speciation is still poorly understood. Here, we report the pattern of genomic differentiation between two Lake Victoria cichlid species. Lake Victoria has dried up and has been refilled roughly 15,000 years ago. This lake harbors several hundreds endemic species of cichlids. They have undergone very recent and rapid speciation events during this short period. These fish species are genetically closely related and share nucleotide polymorphisms among species. So far, only one gene, a long-wavelength sensitive opsin (LWS), was identified as a gene bearing fixed genetic differences between species. Further analysis showed LWS was responsible for adaptation and speciation in cichlids. In this study, we analyzed genomic DNA sequences from two Lake Victoria cichlids (20 individuals each). The genetic differentiation between two species was extremely low, while 21 differentiated regions (DRs: 14~28 kb) with fixed differences were extracted by Fst sliding-window analysis. These regions contained one to three coding genes, one of which included LWS. Several of those genes were associated with vision, development, resistance to hypoxia, and differentiation of sexual traits. The expression level of four genes with fixed differences at upstream of the genes were completely different. Thus, at least the genes in five regions including LWS out of 21 regions were indeed responsible for the species differences, suggesting the genes in DRs may be responsible for the adaptation and speciation of Lake Victoria cichlids.