Little is known about the biology of Burmeister’s porpoises (Phocoena spinipinnis), a small cetacean species endemic to South American waters. Information on stock structure, however, is urgently needed, as the species suffers from considerable mortality due to local fishery activities throughout its distribution range. Using mitochondrial control region sequences and 11 species-specific microsatellite loci, we assessed the genetic differentiation among 118 stranded, incidentally or directly-caught Burmeister’s porpoises from different localities in Peruvian, Chilean, and Argentine waters. F-statistics and Bayesian clustering analyses indicate a major population differentiation along the South American Pacific coast, separating Peruvian from both Chilean and Argentine individuals. Interestingly, this population boundary is consistent with the population structure found in another sympatrically-occurring cetacean species: the dusky dolphin (Lagenorhynchus obscurus). Given that vulnerability to local depletion for South American coastal porpoises and dolphins is probably highest in the Peruvian population (due to high exploitation levels and recurrent El Niño events), the genetic data reported here considerably strengthen the need for conservation efforts focused on regulation of catches in local waters. Moreover, we discuss possible genetic differentiation among Burmeister’s porpoises (i) from the Atlantic and Pacific Ocean and (ii) from different Peruvian harbors. Finally, cross-species amplifications suggest that our newly-developed microsatellite markers will be useful in population genetic studies in the five other extant porpoise species.