set of 165 accessions of Chinese waxy maize including landraces and inbred lines were chosen and analyzed for the genetic diversity with SSR markers. The results showed a wide genetic diversity for ear and starch quality characters in the Chinese waxy maize germplasm. A total of 281 alleles were found at the 60 SSR loci, with a range of 2 to 9 alleles per marker. The average alleles per marker across genotypes were 4.68. The PIC values ranged from 0.332 to 0.860, with an average of 0.690. UPGMA analysis grouped the 165 inbred lines into three groups, which was generally consistent with their known pedigree information and breeder’s experience. The results indicated that most of the modern waxy inbred lines have little relationship with the Southwest Chinese waxy maize landraces, which were regarded as the origin of Chinese waxy maize. It would be very helpful to choose the most genetically distant lines for waxy maize genetic study and hybridization breeding based on grouping of waxy maize germplasm.