We studied the species composition and chromosomal variability of malaria mosquitoes in the Volga Basin (Upper, Middle, and Lower Volga regions). We investigated larvae karyotypes of sibling species of the Anopheles maculipennis group. We calculated the frequencies of chromosomal inversions in the local populations of the dominant species An. messeae. We discovered that karyotypic structure of An. messeae populations depends on landscape-climatic zones. Populations of the Upper, Middle and Lower Volga differ in frequency of chromosome inversions XL, 2R, 3R, and 3L.