The territory of Kyrgyz Republic (or Kyrgyzstan) is interesting from a zoogeographical point of view, as it straddles several major ecoregions: Balkhash Lake basin, Chu River drainage, Lake Issyk-Kul basin, Talas-Ters drainage, Upper Syr Darya system, Upper Amu Darya system and Tarim basin. Species composition of fish faunas of all ecoregions are discussed and endemic species and subspecies listed. The degree of endemism is notable, reaching 55 and 70% in the Talas River and Issyk-Kul Lake ecoregions, respectively. Some aspects of human impact on native fish populations are analysed, including the introduction and establishment of exotic species that dominate some lakes and reservoirs, fisheries and aquaculture. A review of fishery resources management underlines the need to formulate a compromise strategy for the conservation of unique native fish communities, and the development and management of capture fisheries, based on both native and exotic species, and aquaculture in Kyrgyzstan.