Abstract
The aboriginal ichthyofauna of the Balkhash basin consists mainly of endemic fish species. By the end of the last century, indigenous fish species were driven out of Lake Balkhash and the Alakol Lakes remain the largest refuges of aboriginal fish fauna. Knowledge of regularities of the modern distribution of the indigenous fishes is crucial for biodiversity conservation as well as restoring aquatic ecosystems. The modern diversity of fish species was investigated there in this study. Significant changes for the indigenous and some alien fish distributions were revealed in contrast with earlier known data. Canonical correspondence analysis (CCA) was used to study the relationships between habitat characteristics and species abundance. Water mineralization and maximal observed water temperatures were estimated as the main environmental variables in fish distribution at the local scale. Habitat change leads to fish fauna homogenization as a result of rare species extinction and alien penetration. Growing human population and poor water management make the future of the indigenous fishes unpredictable.