A doubled haploid (DH) population, which consists of 120 lines derived from anther culture of a typical indica and japonica hybrid ‘CJ06’/‘TN1’, was used in this study. Ligule lengths of flag leaf were investigated for quantitative trait loci (QTL) mapping using the DH population. Five QTLs (qLL-2, qLL-4, qLL-6, qLL-10 and qLL-12) controlling the ligule length (LL) were detected on chromosomes 2, 4, 6, 10 and 12, with the variances explained 11.4%, 13.6%, 27.8%, 22.1% and 11.0%, respectively. Using four known genes of ZmGL1, ZmGL2, ZmGL3 and ZmGL4 in maize from the MaizeGDB, their homologs in rice were aligned and integrated into the existing simple sequence repeats linkage map by in silico mapping. A ZmLG1 homolog gene, OsLG1 encoding a squamosa promoter binding protein, was located between the markers RM255 and RM280, which is just identical to the interval of qLL-4 on the long arm of chromosome 4. The results are beneficial to dissection of the ligule molecular mechanism and the study of cereal evolution.