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Grain size is one of the most important agronomic traits controlling grain yield. Development of novel germplasm with large grains would be beneficial for crop improvement. We report the genetic identification and functional analysis of the LONG GRAIN 6 (LOG6) gene, which is identical to MITOGEN-ACTIVATED PROTEIN KINASE 6 (OsMAPK6), affecting grain length of rice. Map-based cloning revealed that the long-grain phenotype of log6-D results from a glutamine (E) to lysine (K) mutation in the conserved TEY motif of OsMAPK6. In near-isogenic lines (NILs), the log6-D allele increased grain length and grain yield of Guichao 2 (GC2), Teqing (TQ), and 93–11. Sequence analysis revealed 10 OsMAPK6 haplotypes, with xian (indica) and geng (japonica) harboring different haplotypes. Our findings shed light on the function of MAPKs and offer a novel dominant allele for improving the grain yield of rice.