Mitochondrial diversity in house flies was examined by using the single-strand conformation polymorphism method in house flies, Musca domestica L. sampled in six zoogeographical subregions in the New World. The number of haplotypes and haplotype diversities were homogeneous among subregions, but a strong spatial component was found in the distribution of particular haplotypes. Nei’s differentiation index among subregions, G_RT, was 0.53 and that among populations within subregions, G_PR, was 0.31. Greater genetic differentiation was found among populations in the Nearctic than in the Neotropics. Haplotype frequency distributions in two of three Nearctic subregions deviated from that expected under the neutral infinite allele model, suggesting the existence of differential selection patterns.