The frequencies of disk sequences in the polytene chromosomes from the salivary glands of the larvae of three species of chironomids (Diptera, Chironomidae) are analyzed. Statistically significant deviations of the population structure from the structure expected by the Hardy-Weinberg equilibrium law are detected. The distribution of frequencies in individuals with different levels of heterozygosity in the Camptochironomus tentans populations is examined. The influences of the driving and stabilizing selection on the population’s genotype are uncovered. A methodology for estimating the influence of different disk sequences on the species’ adaptability based on single collections is proposed. The stability of the nonequilibrium in the studied populations is noted and interpreted as a sign of homeostasis.