Zoysia Willd. are warm-season turfgrasses used throughout the southern United States and upward into the transition zone for their superior heat and drought tolerances and their relatively low input requirements. Understanding the population structure present within Zoysia germplasm can assist plant breeders in exploiting available variation. The objectives of this study were to assess simple sequence repeat (SSR) allelic diversity within and among Zoysia spp., evaluate the genetic constitution of putative interspecific hybrids, and determine if Zoysia spp. and hybrids can be differentiated by inflorescence traits. Sixty-two Zoysia accessions selected as a subset of genotypically and phenotypically diverse genotypes were evaluated with 50 SSR markers and six inflorescence traits. Both an unweighted pair group method with arithmetic averaging (UPGMA) phylogram and principal coordinate analysis (PCO) analysis revealed a continuum of genetic variation present within and among the species. The model-based program STRUCTURE revealed two distinct subpopulations within Z. japonica Steud. as well as a distinct Z. matrella (L.) Merr. subpopulation. Based on SSR analysis, 23 Zoysia accessions evaluated had evidence of admixture. Six inflorescence phenotypes also revealed a continuous range of variation. This study was able to verify the presence of hybrids between Z. japonica and Z. matrella and provided further evidence for the hypothesis that Zoysia spp. are subpopulations or ecotypes within one species and not separate species.