The Mongolian Aquatic Insect Survey (MAIS) has systematically surveyed a diverse range of aquatic habitats in Mongolia during the summers of 2003–2006 and 2008–2010. Nymphomyiidae were collected from three sites in the northern Altai region of Mongolia in 2008 and 2010. Collection of this rare family of aquatic Diptera prompted a search through specimen data generated by the MAIS project and by other aquatic ecology projects in Mongolia resulting in a database of 375 sites which had specimens identified to family. No additional nymphomyiid specimens were found, indicating that these flies are rare in Mongolia. Our three sites represent unique, semi-arid and tundra habitats for Nymphomyia. The sites also extend the range of Nymphoymia into central Asia forming an important biogeographic link between extant eastern Palearctic and extinct western Palearctic nymphomyiids.