Single-strand conformation polymorphisms at 16S2 and COII mitochondrial genes were surveyed in 111 housefly samples from North, Central, and South America, Europe, Asia, Africa, and the Western Pacific. Forty-eight phenotypes were detected, of which none were ubiquitous, and 21 (44%) were confined to a single zoogeographical region. Nei's gene diversity index (H(S)) was 0.27 and was heterogeneous among zoogeographical regions. Phenotypes were the most diverse in the Ethiopian region and least diverse in the Palearctic and Nearctic regions. Hierarchical partitioning of the total diversity among regions (Nei's G(RT) = 0.49) indicated only a small proportion was shared. The differentiation of populations within regions (G(SR)) was 0.32. All pairwise estimates of gene flow between zoogeographical regions were less than 0.31 reproducing females per generation (mean 0.19). We conclude that housefly populations are highly structured even though the flies are mobile and easily capable of passive transport by ship and air.