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Indonesia is an archipelagic nation comprising some 17,000 islands of varying sizes and geological origins, as well as marked differences in composition of their floras and faunas. Indonesia is considered one of the megadiversity centers, both in terms of species numbers as well as endemism. According to the Biodiversity Action Plan for Indonesia, 16% of all amphibian and reptile species occur in Indonesia, a total of over 1,100 species. New research activities, launched in the last few years, indicate that these figures may be significantly higher than generally assumed. Indonesia is suspected to host the worldwide highest numbers of amphibian and reptile species. Herpetological research in Indonesia, however, has not progressed at a rate comparable to that of neighboring countries. As a result, the ratio of Indonesian species to the entirety of Southeast Asian and Malesian species has “declined” from about 60% in 1930 to about 50% in 2000, essentially a result of more taxa having been described from areas outside Indonesia. Many of these taxa were subsequently also found in Indonesia. In the last 70 years, 762 new taxa have been described from the Southeast Asia region of which only 262 were from Indonesia. In general, the herpetofauna of Indonesia is poorly understood compared to the herpetofauna of neighboring countries. This refers not only to the taxonomic status, but also to the basic biological and ecological characteristics of most of the species. Moreover, geographic distribution patterns for many species are only poorly known. In view of the alarming rate of forest loss, measures for more effective protection of the herpetofauna of Indonesia are urgently required. The status of virtually all of the Indonesian species, e.g. in terms of IUCN categories, remains unknown, and no action plans have been formulated to date. In addition, research results on Indonesia’s amphibian and reptile fauna have often not been made available in the country itself. Finally, there is a clear need to organize research activities in such a way that a larger segment of the Indonesian population becomes aware of the importance of the herpetofauna as an essential component of the country’s biodiversity. To address these issues, this paper (1) gives an overview of the herpetofauna as part of Indonesia’s biodiversity, (2) outlines the history of herpetological research in the region, (3) identifies major gaps in our knowledge of the Indonesian herpetofauna, and (4) uses this framework for discussing issues and problems of the conservation of amphibians and reptiles in Indonesia. In particular, the contents and shortcomings of compilations of lists of protected or threatened species by national and international authorities are discussed, major threats to the Indonesian herpetofauna or certain components thereof are described, and a set of measures for better longterm conservation is proposed.