The vaquita (Phocoena sinus) is the world's smallest porpoise, and exists only in a single isolated location in the far northern Gulf of California, Mexico. The vaquita is also the most endangered marine mammal, with approximately 10 individuals remaining in 2020 following a steep population decline caused by excess mortality from gillnet fishing. We sequenced whole genomes of 20 individuals to analyze patterns of genome-wide variation in order to study the vaquita's current status, historical abundance, and likelihood of extinction in the near future.