Nannophya pygmaea (commonly known as the scarlet dwarf dragonfly) was designated as an endangered species, level II, by the Ministry of Environment of Korea in 1994; it has been used as a flagship species for the protection and preservation of wetlands. Over 25 sites in Korea have been identified as the habitat of Nannophya pygmaea. However, most of these habitats have proven to be unstable, and there have been subsequent changes in the assemblage structure and organization. Most habitats changed to become grasslands or plain ground, and now only five habitats remain. Although efforts have been made to protect the Nannophya pygmaea as an endangered species, their habitat loss has increased, caused by natural succession and drought. Therefore, we need to make stronger protections in the preservation manual of level II endangered species, particularly Nannophya pygmaea, and its native habitats in Korea.