Pennisetum species are widely used as ornamental grasses and may be a valuable genetic resource for their breeding to broaden its genetic basis. At present, new ornamental Pennisetum cultivars are primarily bred via somaclone, which increases the number of variants. It is difficult to estimate whether the suspected variants are authentic in genetic features by morphological traits because of their many limitations. Moreover, although the phylogenetic classification of the Pennisetum genus has been approved in some morphological and cytological studies, genetic evidence is lacking. In the present study, we developed 15 specific simple sequence repeat (SSR) markers with a large amount of polymorphisms and strong distinguishing abilities for Pennisetum ornamental grasses using magnetic bead enrichment. These markers, together with the other 11 reported polymorphic SSRs, were further used for the identification of a broad collection of 55 Pennisetum samples, including nine original taxa and 46 suspected variants. After comparing the genetic characteristics between each variant and its corresponding original taxon, we verified 20 suspected variants that possess the potential to become new, commercially desirable cultivars. The nine original taxa and the 20 verified variants were identified based on the polymorphisms of six core loci, and unique molecular identities with 15 denary digits for each taxon were further established. The rationality of the traditional phylogenetic classification system of the Pennisetum genus was further verified using 147 polymorphic alleles. The present study promotes the protection, registration, breeding, and international communication of Pennisetum ornamental grasses.