The suborder Mysticeti (whalebone whales) comprises ten extant species. Taxonomic relationships within the suborder were studied by using three non-cross hybridizing highly repetitive DNA components as probes in molecular hybridizations including all ten species. The first component had the same repeat length, 1760 bp, in all species and constituted a large portion of all genomes. The second component occurred in all species of the family Balaenopteridae, rorquals, with a repeat length of almost-equal-to 420 bp. The same repeat length was also found in the gray whale, Eschrichtius robustus, of the monotypic family Eschrichiidae and in the pygmy right whale, Caperea marginata, a species that has usually been included in the family Balaenidae, right whales. The component was also found in the bowhead, Balaena mysticetuts. and in the right whale, Eubalaena glacialis; however, in these species the almost-equal-to 420 bp repeat length did not occur. The third component was present in all balaenopterid genomes and also in the gray whale and the pygmy right whale. The component was virtually nonexistent in the right whale and the bowhead. Thus. at the DNA level, there is a major distinction between the bowhead and the right whale vis-a-vis all other mysticetes including the pygmy right whale. The results support the exclusion of the pygmy right whale from the family Balaenidae.