In this study, the male sterile mutant D63 was isolated from the indica cultivar G46B through ethyl methanesulfonate (EMS) mutagenesis. Furthermore, phenotypic characterization, genetic analysis and gene mapping of the mutant were performed. As result, anthers of the D63 mutant were smaller, thiner and milk white, and there was no pollen in its pollen sac, which belonged to non-pollen type of male sterility. During the mature period, compared with the wide-type parent G46B, plant height and panicle exsertion of D63 reduced by 13.7% and 266.7%, respectively, and selfing seed setting rate is 0. Genetic analysis indicated that male sterility of the D63 mutant was controlled by one pair of recessive nuclear gene. The sterile gene was finally mapped between the InDel markers J2 and J4 on the long arm of rice chromosome 2. The genetic distances from the sterile gene to the two InDel markers were 0.2 cM, 0.1 cM, respectively, and the physical length of this region was 105.8 kb. Sequenceing analysis of the candidate genes in the mutant and its wild-type revealed a single-nucleotide A-to-C mutation existed in the D63 mutant at position 1580 in coding region of the LOC_Os02g28970 gene for secretory fasciclin glycoprotein, which resulted in an amino acid change from His at position 527 to Pro in the encoded product. The D63 mutant has completely no pollen grain in its anthers, but the reported mtr1 mutant had abortive pollen grains. The differenent phenotypes of the two mutants may be caused by different mutational sites of the base sequence of LOC_Os02g28970 gene, and/or different genetic backgrounds of the two subspecies, because the two mutant belonged to indica and japonica subspecies, respectively.