Drosophila prolongata is an unique species not only for their morphology but also for mating and aggressive behaviors. Both females and males of D. prolongata have so-called “picture wing” that is comparable to those of Hawaiian Drosophila, but it is just a one of characters that make D. prolongata special. Only males of D. prolongata have enlarged forelegs, colored in black and white stripe. This male-specific morphology plays a critical role in male’s behaviors, including fight between males, and courtship toward females. Because such morphological and behavioral characters are not observed in the sibling species, rapid evolution of relatively small number of loci might be responsible for D. prolongata evolution. To identify these loci, we are currently performing genome wide analysis using NGS combined with classical genetics. As far as we see the genome sequence, D. prolongata is surprisingly close to D. melanogaster, suggesting that functional examination of genes might be possible.