The vaquita, Phocoena sinus, is one of two critically endangered cetacean species, and is listed as an endangered species in both the United States and Mexico. These listings result from a small population size, estimated to be 224 animals, and a rapid decline in abundance (18% per annum) thought to be caused by human activities. To characterize the genetic composition of the vaquita, we have sequenced a portion of the mitochondrial DNA control region from 43 individuals collected between 1985 and 1993. All animals had identical sequences. While low genetic variability has been reported for cetacean species, this complete lack of polymorphism in the control region is unique. This result is concordant with the hypothesis that the evolutionary history of the species includes a bottleneck or founder event, possibly at species inception, followed by a small long-term effective population size. We recommend parallel studies of nuclear variability, which could provide understanding of the basic biology of the vaquita for use in conservation efforts.