Cercospora sojina (Hara), an air-borne pathogen, infects soybean leaves causing frog-eye leaf spot (FLS). Three major genes (Rcs1-3) underlie resistance to the major races of FLS. However, these genes can be defeated by some races of FLS. Breeding for sustainable resistance to FLS may need loci for tolerance and partial resistance to a broad spectrum of races. However, the genetics of partial resistance appeared to be more complex and hard to breed for. The objective of this study was to identify loci underlying partial resistance to one race of FLS under controlled conditions in a greenhouse. A culture of Cercospora sojina virulent race 2 (ATCC 44531) was used to induce leaf symptoms of one hundred F5:14 RILs derived from the cross of Essex by Forrest. Essex was partially resistant while Forrest was partially susceptible to FLS. The leaf symptoms were measured at 21 dai and 42 dai. There was no significant correlation between FLS severity at 21 and 42 dai (r =0.08 and P= 0.005). There was more variation among lines at 21 dai than 42 dai. At 21 dai there was a major QTL on near Satt319 on LG C2 (chromosome 7; LOD 3.8; R2 15%) where the Essex allele reduced leaf symptoms by 0.7 units. At 42 dai there was a major QTL on near Satt632 on LG A2 (chromosome 8; R2 was 50%; LOD was 3.6) where the Essex allele reduced leaf symptoms by 0.4 units. Neither locus mapped to the location of Rcs3 but might represent alleles of Rcs1 or Rcs2. Since loci were active at one stage of seedling development it was inferred partial resistance to FLS was conditional upon growth stage.