The genetic basis underlying the relationship between the source leaves (the top two leaves) and the sink capacity in rice was investigated in a replicated trial of 2418 F2 derived F4 progeny from an inter-subspecific cross between cv. Lemont (japonica) and cv. Teqing (indica) and a complete linkage map with 115 well distributed RFLP markers. Path analysis indicated that 50% of the phenotypic variation in the primary sink capacity-grain weight per panicle was attributable to variation of the flag leaf area. Thirteen QTL and 30 pairs of epistatic loci were identified, which influence the length, width and area of the source leaves and the size of the primary sink (panicles) panicle length, floret density and floret number per panicle. Two QTL (QLl3b and QLw4) and 7 pairs of epistatic loci are largely responsible for the observed relationship between the source leaves and the sink capacity. The others appear to primarily influence the shape of the source leaves or panicle length/branching, and contribute little to the observed source-sink relationship and partially explain the yield component compensation. Our results suggest that important QTL affecting the source leaves can be manipulated through marker-assisted selection to increase sink capacity, which might result in improved yield potential in rice.