The number of spikelets per panicle in rice is determined by characters of the panicle such as the number of primary branches (PB) and secondary branches (SB) and panicle length (PL). It is a quantitative traits controlled by several genes. In this study, the nucleotide polymorphism and haplotype diversity of coding region of genes related to number of spikelets per panicle (SPP), including APO1, APO2, FON1, DEP1, GN1a, GHD8, HD1, and SP1, were analyzed using 45 varieties which showed significant phenotypic variations for PL, PB, SB and SPP. Significant correlations were observed among all the panicle traits. A total of 151 polymorphisms, including 114 SNPs and 26 indels were detected in coding region of 8 genes which constructed 52 haplotypes. Neutrality tests revealed that population subdivision event or balancing selection occurred in locus of APO2, FON1, and HD1 whereas no significant deviation from neutrality was detected in the other genes, suggesting a neutral evolution. Based on the results of GLM association analysis, 34 polymorphic sites in 6 genes were significantly related with the 4 panicle related-traits.