All living things share some common life processes such as growth and reproduction, and have an ability to respond to their environment. However, each type of organism also has its own specialized way to manage the biological events. Genetic sequences of the organisms determine their phenotypic and physiological traits. Based on the genetic information, comparative genomics have been widely applied to delineate the differences and similarity between various genomes, and significant progress has been made in understanding of regenerative biology by comparing genomes of a variety of the lower animal models of regeneration such as planaria, zebra fishes and newts. However, genome of lizards has been relatively ignored until recently, although the lizards have been studied as an excellent amniote model for tissue regeneration. Very recently, whole genome sequences of the lizards have been revealed, and several attempts have been made to find regeneration factors based on their genetic information. In this article, recent advances in comparative analysis of the lizard genomes are introduced, and their biological implications and putative applications for regenerative medicine and stem-cell biology are discussed.