To characterize habitats of Nannophya pygmaea Rambur (the northern pygmyfly; Odonata: Lilbellulidae), which is endangered in Korea, we analyzed characteristics of surface water and soil, landscape properties, and vegetation types in 22 habitats in eight areas of Korea where nymphs of N. pygmaea have been found since 2005. We divided the habitats into two groups: DS (dwelling site) habitats, where N. pygmaea was observed at the time of the study, and PDS (past dwelling site) habitats, where N. pygmaea recently lived but is no longer found. The habitats were mostly located in former paddy fields on mountain slopes that have been abandoned for 3–7 yr. The main water sources for these habitats were ground water and surface runoff, and the water level was stable at 3–7 cm in depth. The habitats ranged from 300 to 1000 m² and were dominated by Juncus effusus, which formed tussock mounds. According to the hydrosere model of succession, N. pygmaea appeared mostly in the early stages of plant succession (the period ≈3–7 yr after the initiation of succession in former paddy fields) and N. pygmaea preferred habitats displaying the water and soil characteristics that are typical of the early stages of succession in abandoned paddy fields. These results indicate that the primary habitats of N. pygmaea in Korea are recently abandoned paddy fields that are in an oligotrophic state. As succession proceeds in these habitats, N. pygmaea disappears. A habitat management program should be launched to conserve the habitats and populations of N. pygmaea.