Mites of the genus Geckobia (Acariformes: Pterygosomatidae) are permanent ectoparasites of geckos and are useful models for studies of host association and host–parasite coevolution. However, despite the diversity of geckos in Japan, the diversity of Japanese Geckobia remains poorly understood, and only two species have been formally recorded. This study aimed to clarify the species diversity of Japanese Geckobia, to examine their host associations, and to evaluate the potential effects of invasive geckos on native mite assemblages. Field surveys and specimen examinations were conducted using geckos collected from subtropical to temperate regions of Japan, including Okinawa Island, the Tokara Islands, southern Kyushu, and southern Honshu. Both native and invasive host species were examined, including Goniurosaurus yamashinae, Gekko takaraensis, G. japonicus, and G. monarchus. Mite specimens were collected from host body surfaces and examined using light microscopy and scanning electron microscopy. Species were distinguished based on external morphological characters and host records. Preliminary observations of more than 100 mite specimens suggested the presence of multiple undescribed species of Geckobia associated with Japanese geckos. Among these, a probable undescribed species was detected in specimens collected from a gecko host in Okinawa. These findings indicate that the diversity of Geckobia in Japan has been substantially underestimated and that cryptic diversity may be present within morphologically similar populations. Although the present data are still limited, Japanese Geckobia mites may provide a useful system for future studies on host association, cospeciation, and host switching in insular reptile faunas. This study provides new taxonomic information on Japanese Geckobia.