For animals, immunity is an essential function to survive and a fundamental factor to adapt various environments. Evolution of immune-related genes is thus an important factor for diversification of organisms and its genomes. Because of their evolutionary history as the earliest terrestrial tetrapods and adaptation to both aquatic and semi-aquatic life through metamorphosis, amphibians is one of the key organisms for understanding evolution of genes related to acquired and natural immunity in vertebrates. Moreover, their immunity-related genes have been paid attention in the context of conservation genetics due to emergence of amphibian fungal pathogen. We therefore, sequenced skin and spleen transcriptomes of eight endangered amphibians (7 anurans: Odorrana splendida, O. ishikawae, O. amamiensis, O. narina, O. supranarina, Babina subaspera, and B. holsti and a urodele: Echinotriton andersoni) in Ryukyu archipelago in Japan and compared expression patterns and repertoire of the genes. As the results, the highly expressed genes were similar between species, and multiple antimicrobial peptides were identified in skin transcriptomes of each species.