A yellow-green leaf mutant, named ygl15, was identified from the hybrid progeny of indica rice lines. Phenotype identification and gene mapping were performed in this study to clarify the leaf color variation mechanism of the ygl15 mutant. The results showed that yellow-green leaves appeared in the ygl15 mutant at the seedling stage, meantime the chlorophyll and carotenoid contents in leaves decreased significantly compared with the wild type. The agronomic characters of the ygl15 mutants were affected. The plant height, the effective panicle number, the total grain number per plant, and the filled grain number per plant decreased. While the panicle length, the grain number per panicle, and the seed setting rate kept stable, and the thousand-grain weight increased slightly. Gene expression analysis suggested that, the expressions were up-regulated for genes related to chlorophyll synthesis and photosynthetic system but down-regulated or stable for genes related to heme synthesis in the leaves of ygl15 mutant. Genetic analysis showed that the mutant phenotype of ygl15 was controlled by a single nuclear recessive gene. Using the F2 population of the ygl15 mutant crossed with Zhonghua 11, the ygl15 gene was located within a 79 kb region between markers M08124 and M08175 on the third chromosome of rice through the preliminary mapping and fine mapping. This study laid a solid foundation for further cloning ygl15 mutant gene and studying gene function.