I assessed the systematics of Ammospermophilus leucurus from the islands of Espíritu Santo and San Marcos adjacent to the Baja California peninsula, using sequences of the mitochondrial cytochrome-b (Cytb) gene and morphological analyses from the island and the peninsular samples. For the molecular analysis, the Cytb gene (500 base pairs) was sequenced from individuals from 34 different localities. Maximum-parsimony, maximum-likelihood, and neighbor-joining analyses indicated a phylogenetic break in the central part of the Baja California peninsula. Samples from the islands of Espíritu Santo and San Marcos were grouped with the southern clade with an average of 1.2 substitutions that separated adjacent haplotypes in a network. Two haplotypes occurred on San Marcos Island; one was unique and the other also was present in peninsular samples. The only haplotype found on Espíritu Santo Island also occurred on the peninsula. Both univariate and multivariate morphometric analyses and the pattern of presence–absence of the 3rd upper premolar distinguished samples from Espíritu Santo and the Cape region of the peninsula but not between San Marcos Island and Francisco de la Sierra on the peninsula. Thus, the San Marcos Island ground squirrel could not be distinguished from those of the peninsula and should be recognized as the same subspecies that occupies the adjacent peninsular areas (A. leucurus extimus). In addition, neither molecular nor morphological data supported the recognition of A. insularis (from Espíritu Santo Island) as a distinct species from peninsular samples of A. leucurus, although this taxon showed morphological differentiation in dental characters that still support its recognition as a valid subspecies (A. leucurus insularis).