A doubled haploid population derived from anther culture of ZYQ8/JX17 F(1), a typical indica and japonica hybrid, was used in this study. Morphological index and its related taxonomic traits were investigated in 121 DH lines. The quantitative trait loci (QTLs) for morphological index and its related taxonomic traits were analyzed. Two major QTLs for leaf hairiness, three QTLs for length/width of grain, one QTL for color of hull when heading, one QTL for hairiness of hull, two QTLs for length of the first and second panicle internode, and one major QTL and two QTLs for phenol reaction were detected. Four QTLs for morphological index were also identified on chromosomes 1, 3, 4 and 6, respectively, three of which on chromosomes 1, 3 and 6, respectively, were found to be located in the same chromosome regions where some QTLs for the related taxonomic traits were located.