In this study, six panicle traits of 98 foxtail millet cultivars were investigated and genome re-sequencing was performed for the 98 foxtail millet cultivars. Totally 4 482 208 SNPs were developed by re-sequencing of the 98 foxtail millet cultivars. Genome-wide association analysis between SNPs and panicle traits showed that 118, 83, 97, 13, 54 and 458 SNPs were associated with panicle length, panicle diameter, branch number per panicle, panicle weight, grain weight per panicle and 1 000-grain weight respectively. The SNPs associated with panicle length, branch number per panicle, grain weight per panicle and 1 000-grain weight distributed on all of the nine chromosomes, while the SNPs associated with panicle weight distributed on the six chromosomes except Chr.1, Chr.2 and Chr.5 and the SNPs associated with panicle diameter distributed on the eight chromosomes except Chr.6.