Dry direct seeding method can effectively reduce human/resource consumption. Mesocotyl length （ML） affects the emergence and seedling vigor of dry direct seeding rice. Cultivating long ML varieties is the most economical and effective way to promote the popularization of the dry direct seeding method. Dry direct seeding has been popularized in Indica rice areas in South Asia and Southeast Asia， but less in Japonica rice areas. A number of candidate genes related to mesocotyl elongation have been found， but their reliability and applicability remain yet to be verified. Based on 97 identified candidate genes that modulate the mesocotyl elongation， we carried out candidate genes association analysis in two natural populations of Japonica rice， TROP and TEMP. Four significant candidate genes were identified， and each explained 4.7%-6.3% and 5.4%-6.7% phenotypic genetic variation in TROP and TEMP， respectively. Of these， three genes LOC_Os01g44130， LOC_Os03g50560 and LOC_Os05g27790 were identified in both populations， while LOC_Os11g10990 and LOC_Os10g20860 were detected in the TROP and TEMP populations， respectively. The deduced proteins are annotated mainly involving in plant hormone synthesis and metabolism， signal transduction and plant growth process. Six and three superior haplotypes with potential used for molecular marker assisted breeding were further identified in TROP （LOC_Os05g27790-Hap3 and LOC_Os05g27790-Hap6， LOC_Os03g50560-Hap1， LOC_Os01g44130-Hap1 and LOC_Os11g10990-Hap1 and LOC_Os11g10990-Hap3） and TEMP （LOC_ Os05g27790-Hap6， LOC_Os01g44130-Hap1 and LOC_Os10g20860-Hap5） populations. Collectively， these genes and their corresponding superior haplotypes identified in this study can be applied to the molecular breeding of rice varieties with long mesocotyl.