Mo17 and SH15, two head smut resistant inbred lines as donor parents were chosen to produce BC3F1 and BC4F2 populations of Huangzao4 ×(Huangzao4×Mo17) and Chang7-2 ×(Chang7-2×SH15) with two susceptible inbred lines Huangzao4 and Chang7-2 as recurrent parents, respectively. These populations were evaluated for head smut resistance with artificial inoculation under field condition. The disease incidence for BC4F2 populations of Huangzao4 ×(Huangzao4×Mo17) was higher than that of BC3F1 population. The disease incidence was found different for the BC4F2 populations of Huangzao4 ×(Huangzao4×Mo17) and Chang7-2 ×(Chang7-2×SH15). The resistant individuals were genotyped by SSR markers on maize bins 2.09 and 3.04. The number of donor introgrssion segments in BC4F2 resistant plants was becoming less than that in BC3F1, and also was different in different populations. Using linkage disequilibrium analysis, two major QTL for head smut resistance were identified, each on bin 2.09 and bin 3.04, with linked markers umc2077 and phio53\bnlg1965, respectively. The results obtained provided both useful genetic information and materials for QTL mapping and marker assisted selection for head smut resistance in maize.