Post-marital residence of spouses is one of the architects of population genetic structure. In the present study, we tested how the place of residence of males and females in Ngazidja, Comoros Islands, has unequally channeled, by dispersal among villages, the male and female genetic diversity. Using sequences of the hypervariable segment I of the mitochondrial DNA (mtDNA HVS-I) and six Y-chromosome microsatellites (Y-STRs), we measured the genetic variation and male-to-female effective number of migrants ratios based on FST values and revealed a genetic structure mostly driven by male gene flow across villages. This genetic feature illustrates the uxori-matrilocality inherited from the Bantu expansion, though one exception exists in Bandamadji whose historically documented military status implied patrilocality in this locality.