Polyteny is an effective mechanism for accelerating growth and enhancing gene expression in eukaryotes. The purpose of investigation was to study the genetic variability of polyteny degree of giant chromosomes in the salivary glands of Drosophila melanogaster Meig. in relation to the differential fitness of different genotypes. 16 strains, lines and hybrids of fruit flies were studied. This study demonstrates the significant influence of hereditary factors on the level of polytenization of giant chromosomes in Drosophila. This is manifested in the differences between strains and lines, the effect of inbreeding, chromosome isogenization, hybridization, adaptively significant selection, sexual differences, and varying degrees of individual variability of a trait in different strains, lines, and hybrids. The effect size of the genotype on the degree of chromosome polyteny in Drosophila salivary glands was 45.3%, the effect size of sex was 9.5%. The data obtained allow us to conclude that the variations in the level of polyteny should be considered as a manifestation of the structural and functional polymorphism of giant chromosomes, which is an essential factor in the differential fitness of flies and has a selective value.