Hairs on the leaf are an important agronomic characteristic for rice growth and farming. The segregation ratio of pubescence in the F₂ population showed that the pubescence on the leaf is controlled by a single dominant gene. Fine mapping for the gene was carried out by producing an Indel (insertion-deletion) primer based on BSA-Seq data. Results of the analysis revealed within the candidate site the presence of HL6, a published pubescence gene. By haplotype analysis of HL6 in the core-collection data, SNPs were found in HL6’s exons between the plants. These sequence variations can be useful for marker-assisted selection.