This report presents the results of a comparative molecular cytogenetic analysis using the DNA probes for ancient and modern human genomes on metaphase chromosomes by the fluorescent in situ hybridization (FISH). FISH of ancient and modern human DNA probes identified specific signals in the C-positive blocks of the pericentromeric chromosomal regions. The most intense signals were detected on chromosomes, which are characterized by the largest C-heterochromatin blocks, i.e. in the centromeric regions of chromosomes 1, 9, 16 and 19. Simultaneous hybridization of two DNA probes of ancient and modern human has identified a difference in the intensity of the observed FISH signals that may be associated with quantitative differences in DNA sequences homologous to the C-positive regions of the chromosomes in the genomes of modern and ancient man. Significantly more robust quantitative differences were found between ancient and modern human DNA probes when heterologous chromosome painting was applied for metaphase chromosomes of chimpanzee (Pan troglodytes) and gibbon (Hylobates lar). In general, the data indicate a similar structural organization of chromosomal domains (e.g., occupied by centromere alpha and classical satellite DNA families) in modern Homo sapiense sapiens and Archaic Homo sapiense denisovan. The data collaborate with our deep-sequencing analysis of DNA repeat families of genomes of archaic-modern hominins (upublished). To our knowledge, this is the first study of chromosomal genomic organization of extinct species using cytogenetic approach with ancient DNA.