Populations of the genus Gekko from three southern islands of the Tokara Group, Ryukyu Archipelago are known to be unique in lacking distinct preanal pores even in adult males. Recently, we found an almost identical morphotype from five islands of the Amami Group, where only G. hokouensis, a species having distinct preanal pores in adult males, has hitherto been recorded. To clarify the taxonomic status of these poreless geckos from the Tokara and Amami Groups, we conducted allozyme and morphological comparisons of Gekko specimens collected from these eight islands and one adjacent island. Results of the allozyme analyses showed the presence of fixed allelic differences at 7–14 loci between samples of the poreless form and sympatric G. hokouensis from each of the Amami islands, confirming their reproductive isolation. Our data further revealed the presence of two genetically divergent groups within the poreless form that are distinct from each other by fixed allelic differences at no less than 30% of loci examined. Ranges of these two groups are contiguous with each other but do not overlap on a single island. Distance analysis showed that one of the two groups is genetically much closer to G. hokouensis than to the other. These results strongly suggest that each of them represents an evolutionarily independent unit and deserves recognition as a full species. We describe these species based on a set of characters that clearly discriminate them from all other congeneric species hitherto described, and we briefly discuss their historical biogeography.