The Commerson’s dolphin, Cephalorhynchus commersonii, is found in shallow waters of the continental shelf off the eastern coast of South America between 40°S and 56°S. This species is taken incidentally in artisanal gillnet fisheries, especially along the shallow coastline of northern Tierra del Fuego and southern Patagonia. The biological importance of by-catch is likely to be underestimated if the boundaries of subpopulations are not properly defined. Here, we report on the sequence variation of the mitochondrial DNA control region of the Commerson’s dolphin from five areas defined in Tierra del Fuego, Argentina and Chile, to provide a preliminary assessment of population structure where conservation efforts are most needed. A 466 bp fragment of the mitochondrial DNA control region was sequenced from 196 samples of skin, teeth and bone, defining 20 haplotypes from 17 polymorphic sites. Nucleotide (π = 0.40%) and haplotype (h = 0.807) diversity were low compared to some other odontocete populations, but similar to that of other species of this genus. Genetic differentiation evaluated through analyses of molecular variance (AMOVA) showed significant overall differences among areas within Tierra del Fuego (Φ ST = 0.059, P < 0.01). An analysis of sex-specific population structure suggested that the dispersal rates of both females and males are low, indicative of females displaying greater site fidelity. The results from mtDNA control region sequences alone revealed significant differentiation among studied areas, which should be considered as independent management units. We recommend that the impact of localized gillnet mortalities should be managed on a local scale in these areas of Tierra del Fuego.