Population genetic structure was characterized in Xantus's Murrelet (Synthliboramphus hypoleucus) by analyzing variation in the mitochondrial control region (505 samples) and 12 microsatellite loci (428 samples) in birds captured at all 13 current breeding areas in southern California and northwestern Baja California, Mexico. The two types of molecular markers were consistent in revealing strong genetic differentiation between the two currently recognized subspecies (S. h. hypoleucus and S. h. scrippsi) and little or no differentiation among breeding areas within subspecies. Estimates of gene flow were essentially zero, and no evidence for admixture was found. Gene flow among breeding locations within subspecies, on the other hand, was seemingly high. Given these genetic results, as well as clear morphological differences between the subspecies and the apparent lack of interbreeding at breeding areas where the two forms are sympatric, we suggest that two species be recognized. Both forms are genetically distinct from Craveri's Murrelet (S. craveri), a closely related species whose breeding range partially overlaps that of Xantus's Murrelet. Taxonomic subdivision of Xantus's Murrelet introduces new conservation concerns, especially for S. h. hypoleucus, which urgently requires greater study and protective efforts.