Using RAPD markers, polymorphism and differentiation of genomic DNA was examined in seven natural populations of Chironomus plumosus from Europe, Siberia, and North America. All these populations showed high polymorphism of genomic DNA. The Palearctic and Nearctic populations of this species were not statistically significantly different in the genomic DNA polymorphism level. The genetic distance (GD), which characterizes the extent of intraspecific differentiation of population genetic structure, was determined among the natural populations of C. plumosus. The genetic distance was on average 0.0245. It was demonstrated that genetic structures of the Palearctic and Nearctic populations of C. plumosus was differentiated to a higher extent than in Palearctic. However, the genetic distances between the populations from different zoogeographical zones (0.313) did not exceed the level characteristic of the among-population differences, which do not disturb the species genetic integrity.