Abstract The influence of natural mycoflora on population densities of Heterodera glycineswas evaluated in soil from five field sites; two of the fields were planted with soybean and the other three fields had no history of soybean cultivation. The soil samples were either treated with microwave heating for 4 min or left untreated, placed in pots, planted to soybean, inoculated with second-stage juveniles, and maintained in a greenhouse. The nematode population densities and fungal colonization of nematode cysts and eggs were determined 14 weeks after inoculation. The nematode densities in treated soil were 4-fold higher for second-stage juveniles, 4.3-fold higher for cysts, and 7.1-fold higher for eggs than those in untreated soil. The number of eggs produced per female was 73% higher in treated soil compared with untreated soil. The percentages of cysts colonized and index of fungal parasitism of eggs were lower in soil treated with microwave heating than in untreated soil. The nematode population density was negatively correlated with both percentage of cysts colonized by fungi and index of fungal parasitism of eggs. However, no differences in nematode densities, frequencies of fungal colonization of cysts, or index of fungal parasitism of eggs in soil were observed among the five sites.