Objectives: To discover and develop large-scale SSR markers of the P. miliaceum genome, which can be used in future genetic studies effectively.Result: 223,894 putative SSR sequences were identified by next-generation sequencing. A total of 56,694 primer pairs were successfully designed and 240 primer pairs were randomly selected for effectiveness validation. The expected heterozygosity and observed heterozygosity varied from 0.0447 to 0.7713 and from 0 to 0.9545, respectively and the mean of Shannon information index (I) was 0.7254. A UPGMA dendrogram indicated the high quality and effectiveness of these novel genomic SSR markers developed via next-generation sequencing technology. Conclusion:A large repertoire of SSR markers were successfully developed by next-generation sequencing of the P. miliaceum genome which will be useful for the construction of genetic linkage maps, the identification of QTLs, and marker-assisted selection breeding.