A residual heterozygous line (RHL) carrying a heterozygous segment between two SSR loci RM11 and RM134 on the rice chromosome 7 was selected from a set of recombinant inbred lines from the cross D50 (javanica)/HB277 (indica). The former parent produces much longer grains than the latter. Selfed progenies of this selection were analyzed genotypically (SSRs) and phenotypically (grain length). Grain length was discontinuously variable in the mapping populations, allowing for the placement of this QTL qGL7-2 within a approximately 4.8 cM interval defined by RM351 and RM234. A set of new markers within this region were developed, which narrowed the QTL to a 278 kb region defined by the markers Indel1 and RM21945. This region contains 49 predicted genes. The results also suggest that the novel allele for grain length will be used for the application of marker assisted selection for the improvement of grain length.