This study reported the identification of a naturally-occurring mutant app1 which shows abnormal (shorter than the lemma, resulting in the unclosed shell or two palea) or absent palea at the reproductive stage. If compared with wild type, this mutant showed 55.52% of the pollen fertility, 6.48% of the seed setting rate, 10.811 gram of the thousand-grain weight as well as 55.21% of the seed germination rate. By generating the F1 and F2 populations crossed with Nipponbare, F1 plants was observed with a wild-type phenotype and F2 individuals were found with a 3:1 segregation, thus indicating that the app1 mutant phenotype is controlled by a single recessive nuclear gene. Genetic mapping suggested that app1 was located on chromosome 3, flanked by molecular markers ID4231 and ID4246, with a genetic distance of 1.3 cM which corresponds to a physical distance of 13.2 kb. The physical interval contained a single complete open reading frame gene LOC_Os03g11614 in which a point mutation and a 245 bp deletion were detected in the promoter region. RT-qPCR analysis revealed a reduction on the transcriptional level in app1 mutant, thus implying that LOC_Os03g11614 is the most strong candidate. LOC_Os03g11614 was known to encode for OsMADS1 that regulates the development of rice floral organs. Mutations in positions led to various phenotypic variations such as leafy glumes, sterility, and smaller grain size. By taking use of 3000 rice seed resources SNP/INDEL mutation database, the mutation in the app1 promoter of OsMADS1is unique and a novel allele, which particularly resulted in a reduction on gene expression. Thus, this study provided a new germplasm resource which is useful to decipher the OsMADS1 function in the formation of rice floral organs.