Although the Odonata are common inhabitants of various extreme environments such as geothermal springs, brackish wetlands, mangroves, and volcanic lakes, the assemblages of this group associated with extreme habitats in Australasia are rather poorly known. Here, we combine museum collection data and published reports on Odonata from extreme habitats on Flores Island, Lesser Sunda Archipelago. The highly acidic Sano Nggoang Crater Lake (mean pH = 3.17) on Flores houses seven species as follows: Agriocnemis pygmaea, Xiphiagrion cyanomelas (Coenagrionidae), Neurothemis ramburii, Orthetrum pruinosum pruinosum, O. sabina, O. testaceum soembanum (Libellulidae), and Anax gibbosulus (Aeshnidae). A coastal marsh site with slightly brackish water on Flores harbors at least five dragonfly species as follows: Diplacodes trivialis, Neurothemis intermedia excelsa, N. terminata, Pantala flavescens, and Rhyothemis phyllis ixias (Libellulidae). The migratory dragonfly Pantala flavescens was a single species recorded on the waterless Kanawa Island near the western edge of Flores. Our findings suggest that extreme habitats in eastern Indonesia primarily colonized by widespread generalist Odonata species. Finally, an updated checklist of Odonata species recorded from Flores Island was compiled. Our survey of museum specimens recovered two species not found on existing species lists for Flores: Neurothemis intermedia excelsa and Pantala flavescens.