In the housefly, Musca domestica L., sex is usually determined by a dominant factor, M, located on the Y chromosome. However, there are ‘autosomal male’ (AM) populations in which the M factor is located on one or more of the five autosomes (I–V) or on X. We examined changes in the frequency of AM and YM males in North Carolina populations of houseflies after 4 years in the laboratory (NC Lab 02:06) and after 4 or 5 years in the field (NC 2006 and NC 2007). In 2002, 77·7% of the male houseflies were III/III;XYM, 20% were IIIM/III;XX, and 2·3% were IIIM/III;XYM. After 4 years in the laboratory, IIIM/III males disappeared and 17·4% of the males were XMYM. Conversely, 4 years later, the field population was relatively unchanged from 2002. Thus, there was a strong selection against IIIM/III males in the laboratory, but not in the field. Field-collected flies from 2007 indicated a slight increase in the frequency of XYM males and a slight decrease in the frequency of IIIM/III males (relative to 2002 and 2006), suggesting that the relative frequency of XYM and IIIM/III can vary slightly over time in field populations. The detection of XMYM males in 2007 offered the opportunity to evaluate the frequency of the female-determining FD factor, which was found to be present in both the laboratory and field populations, but frequencies varied greatly. The present study represents the first report of FD in houseflies from North America. The significance of these results, relative to observed clines in AM versus YM males, is discussed.