The spikelet number per panicle (SPP) in rice is a quantitative trait controlled by numerous genes. To identify the alleles of these genes, we conducted sequencing of coding region or UTR of 13 genes which are known for controlling SPP trait, subjected to 48 rice cultivars covering 27 Indica, 17Japonica, and 4 Tongil types. The genes were EP3(ERECT PANICLE 3), RCN1(REDUCED CULM NUMBER 1), RCN2(REDUCED CULM NUMBER 2), FZP(FRIZZY PANICLE), LAX1(LAX PANICLE 1), MOC1(MONOCULM 1) APO1(ABERRANT PANICLE ORGANIZATION 1), APO2(ABERRANT PANICLE ORGANIZATION 2), DEP1(DENSE AND ERECT PANICLE 1), FON1(FLORAL ORGAN NUMBER 1), GHD8(GRAIN NUMBER, PLANT HEIGHT, AND HEADING DATE 8), GN1A(GRAIN NUMBER 1A), and HD1(HEADING DATE1). As a result, 1 synonymous SNP was found in EP3, RCN1 and RCN2. In LAX1 and MOC1, 1 non-synonymous SNP was identified. But none of SNP was found from the coding region of FZP. Moreover, 3, 6, 7, 8, 9 and 10 alleles were detected in APO1 and APO2, FON1, GHD8, GN1A, DEP1, and HD1 respectively. The multiple regression analysis revealed that GHD8, DEP1 and HD1 had strong effects on spikelet number of primary branch. In addition, HD1 had strong effects on spikelet number of secondary branch, and for total spikelet number per panicle as well. This work was supported by a grant from the Next-Generation BioGreen 21 Program (Plant Molecular Breeding Center No. PJ008125), Rural Development Administration, Republic of Korea.