The house mouse Mus musculus is a polytypic species, distributed worldwide, with three main subspecies: M. m. musculus in the North-East of Eurasia, M. m. castaneus in South-East Asia, and M. m. domesticus in Europe, the Near-East, and Africa. This last subspecies may also be found in Australia and the Americas, where it was brought by European colonization. Previous studies, however, have shown the presence of specific antiviral determinants of Asian origin in a mouse population at Lake Casitas, California. In this study, an analysis of the variability at 35 enzyme loci demonstrates the hybrid nature of this Californian population intermediate between M. m. castaneus and M. m. musculus. Restriction fragment length polymorphisms of two fragments of the mitochondrial DNA also confirm unambiguously the presence of two types of matrilines in comparable frequencies in our sample. Nevertheless, the study of a subspecies-specific Y chromosome microdeletion in the Zfy2 gene reveals only the M. m. domesticus haplotype at Lake Casitas, a phenomenon comparable with the one observed in other hybrid zones of the M. musculus complex. These findings testify once more that genetic exchanges between subspecies inside the broader M. musculus gene pool are still possible.