The genus of honeypot ants Myrmecocystus Wesmael, 1838 (Hymenoptera: Formicidae) is in the subfamily Formicinae and has 29 described species exclusively from North America, of which 16 are native to the Baja California Peninsula of Mexico. The genus includes mainly arid-adapted species found in habitats such as semi-deserts or coastal dunes. We present a new species, Myrmecocystus baja n. sp., which is morphologically similar to M. intonsus but has less pilosity and a dark reddish head. In addition to diagnostic morphological characters, we also provide evidence based on molecular data, which confirms veracity and distribution of the new species. A Bayesian phylogeny is based on the mitochondrial Cytochrome Oxidase subunit I (COI) gene of the new species, as well as other species of the genus, and shows that individuals from coastal dunes between latitudes 30.5 and 26.5 degrees N form a monophyletic group representing the new species herein described. Additionally, we provide information on nest and colony structure of Myrmecocystus baja n. sp., notably the absence of replete workers, which the genus is known for. In conclusion, Myrmecocystus baja n. sp. is endemic to Baja California and adapted to living in coastal dunes of the Pacific Coast.