Presently, there is no information about the functionality of the immune system in the franciscana dolphin (Pontoporia blainvillei), a small dolphin from southern Brazil. As in the case of the franciscana, the population of southern right whale (Eubalaena australis) which inhabits Brazilian waters has not yet been surveyed in what concerns MHC expression. For the first time it was possible to observe the DQB gene expression in skin of these two species of cetacean using RT-PCR. Skin pieces of the animals were collected to RNA extraction. The fragment corresponding to DQB exon 2 was amplified, cloned and sequenced. A total of five alleles were found, one to franciscana and four to southern right whale. The observed dN/dS ratio of 2.77 (P = 0.03) suggests that this gene is under balancing selection pressure (positive Darwinian selection). The sequences indicate that, in both species analysed, the DQB gene is functional.