Mesocotyl is an essential organ of rice for pushing buds out of soil and plays a crucial role in seeding emergence and development in direct-seeding. Thus, identify the loci associated with mesocotyl length (ML) could accelerate breeding progresses for direct-seeding cultivation. Mesocotyl elongation was mainly regulated by plant hormones. Although several regions and candidate genes governing ML have been reported, the effects of them in diverse breeding populations were still indistinct. In this study, 281 genes related to plant hormones at the genomic regions associated with ML were selected and evaluated by single-locus mixed linear model (SL-MLM) and multi-locus random-SNP-effect mixed linear model (mr-MLM) in two breeding panels (Trop and Indx) originated from the 3K re-sequence project. Furthermore, superior haplotypes with longer mesocotyl were also identified for marker assisted selection (MAS) breeding. Totally,LOC_Os02g17680(explained 7.1-8.9% phenotypic variations),LOC_Os04g56950(8.0%),LOC_Os07g24190(9.3%) andLOC_Os12g12720(5.6-8.0%) were identified significantly associated with ML in Trop panel, whereasLOC_Os02g17680(6.5-7.4%),LOC_Os04g56950(5.5%),LOC_Os06g24850(4.8%) andLOC_Os07g40240(4.8-7.1%) were detected in Indx panel. Among these,LOC_Os02g17680andLOC_Os04g56950were identified in both panels. Haplotype analysis for the six significant genes indicated that haplotype distribution of the same gene varies at Trop and Indx panels. Totally, 8 (LOC_Os02g17680-Hap1andHap2,LOC_Os04g56950-Hap1,Hap2andHap8,LOC_Os07g24190-Hap3,LOC_Os12g12720-Hap3andHap6) and six superior haplotypes (LOC_Os02g17680-Hap2,Hap5andHap7,LOC_Os04g56950-Hap4,LOC_Os06g24850-Hap2andLOC_Os07g40240-Hap3) with higher ML were identified in Trop and Indx panels, respectively. In addition, significant additive effects for ML with more superior haplotypes were identified in both panels. Overall, the 6 significantly associated genes and their superior haplotypes could be used to enhancing ML through MAS breeding and further promote direct-seedling cultivation.