Studies on polytene chromosomes of ovarian trophocytes in malaria mosquitoes revealed significant variation of the structure of pericentromeric heterochromatin (PH). Variations in the number and size of pericentromeric alpha-heterochromatin blocks, puffing and interaction with the nuclear envelope of beta-heterochromatin, and the degree of asynapsis between pericentromeric regions of homologues were detected. Interspecific differences are characteristics of all three chromosomes of Anopheles maculipennis and seem to be directly associated with systemic mutations determining speciation.