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Previous research shows little haplotype diversity in small geographic areas, such as islands and areas where physical barriers interrupt gene flow. The general pattern is the presence of a small number of haplotypes spread across sampling sites. Instead, this paper reports the presence of a large number of haplotypes (Cytb and COI) in the extremely small distribution area (Los Planes basin, Baja California Sur, Mexico) of the Cerralvo pocket mouse, Chaetodipus siccus. Haplotype zoning revealed that haplotypes considered as ancestral are located to the periphery of the distribution area, whereas derived haplotypes are located to the center of the distribution range. Most derivatives are unique haplotypes and many of them exhibit a remarkable characteristic: a separation of not more than 1.7 km between them, which prompts a genetic microstructured population. All these features suggest the presence of a strong philopatric behavior among females.