We evaluated systematic relationships among most of the subspecies of the long-haired sigmodontine mouse Abrothrix longipilis in Chile. We sequenced the complete cytochrome-b gene and 634 base pairs of intron 7 of the β-fibrinogen gene from specimens from 17 localities along the distributional range of A. longipilis. Phylogenetic analyses confirm Abrothrix sanborni, once considered a subspecies of A. longipilis, as a valid species. In the latter taxon we obtained a structured phylogenetic pattern that recovered most of the geographic races traditionally recognized for this mouse. However, strong differentiation was found between A. l. longipilis from Mediterranean Chile and subspecies from the Temperate and Patagonian Forests in the south, suggesting that the former could constitute a different species. We concluded that historical events (glaciations), coupled with local selection pressures (different ecogeographic zones), might account for the current geographic pattern of variation in A. longipilis.