The ambient temperature is a primary factor limiting performance and survival of ectotherms, and thus, thermal adaptation is a fundamental process for their life. In Cuba, three Anolis lizards, A. sagrei, A. homolechis and A. allogus, are known to exist by segregating thermal microhabitat. Although they inhabit the same forest structural microhabitat and have similar morphology and behavior, they show different thermal preference. In fact, A. sagrei inhabits fully sunlit forest, being hot adapted species. A. homolechis and A. allogus inhabit filtered sunlit and shaded forests, being intermediate temperature and cool adapted species, respectively. However, genetic bases underlying their thermal adaptation to different temperature are not fully understood. As the first step of understanding these genetic bases, we determined whole genome sequences of these three species using the next generation sequencer and compared the differences in temperature-related traits, such as transient receptor potential ion channels and heat shock transcription factors.