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This study aims to excavate the SNP loci and candidate genes significantly associated with the seed number per silique (SPS) in Brassica napus L. Having 300 B. napus inbreeding lines as experimental materials, we investigated the phenotypes of SPS under two locations （Jiangxi Agricultural University (JXAU) in Nanchang and Jiangxi Institute of Red Soil (JXIRS) in Jinxian in a year. Then we conducted the genome-wide association study via general linear model( GLM) and mixed linear model (MLM)combining 201 817 SNPs markers determined previously. And finally we predicted the functions of relevant candidate genes within the 100 kb region flanking trait significantly associated SNP loci. The results showed that the broad phenotypic variations of SPS in the two locations among the 300 300 B. napus samples existed, and two germplasm with more SNP were screened. Total 39 SNPs loci remarkably associated with SPS were excavated by general linear model (GLM). Furthermore, 3 SNPs of SPS were detected severally using the mixed linear model (MLM), and they all were detected using GLM. And 19 candidate orthologous genes to documented Arabidopsis the seed number per silique, like CIK, ERF022 and EDE1, were found near our eight SNPs loci. The results are conducive to analyzing the genetic basis of SPS of rapeseed and would lay a foundation for studying the regulation mechanism and guiding the genetic improvement of SPS. [ABSTRACT FROM AUTHOR]