Green rice leafhopper (GRH, Nephotettix cincticeps Uhler) is a serious insect pest of rice in the temperate regions of Asia. Myanmar has a high genetic diversity and is located at the center of the origin of rice. To understand the genetic architecture of GRH resistance in Myanmar indica rice landraces, a genome-wide association study (GWAS) was performed using a diversity panel collected from diverse geographical regions. Phenotypic variation in GRH resistance was associated with three genomic regions, MTA4, MTA5, and MTA11, located on chromosomes 4, 5, and 11, respectively. MTA4 and MTA5 were adjacent to the known resistance genes GRH6 and GRH1. Analysis of haplotypes and linkage disequilibrium blocks revealed that the haplotypes HapGRH6A, HapGRH1A, and HapMTA11A mainly explained GRH resistance. Map-based cloning revealed that GRH6 was highly induced by GRH infestation and conferred resistance by inhibiting the sucking of phloem sap. The distribution of resistance haplotypes revealed that accessions harboring major resistance haplotypes (HapGRH6A and HapGRH1A) were mainly distributed in Southern Myanmar, and HapMTA11A was mainly responsible for GRH resistance in mountainous areas of Myanmar. Our findings could facilitate the elucidation of the molecular mechanism of GRH resistance and provide essential haplotype-based genetic information for the development of GRH-resistant rice cultivars.