The coccidium Sarcocystis singaporensis (Apicomplexa: Sarcocystidae) is a cyst-forming parasite with potential as a biological agent for the control of wild populations of rodents in non-native environments. Phylogenetic analysis based on the ssrDNA supports S. singaporensisisolates as a sister species to sarcosporidians transmitted between snakes and rodents but an association with the carnivore-ruminant Sarcocystis spp. could not be rejected by likelihood ratio tests. Four complete and six partial ssrDNA sequences representing this species are monophyletic in any tree reconstruction method; however, they possess very high pairwise distances of up to 0.053. The obtained sequences suggest the probable existence of at least two divergent paralogous ssrDNAs. Moreover, our results support the co-evolution of lsrDNA and ssrDNA in S. singaporensis. The utility of coccidian lsrDNA and ssrDNA for evolutionary studies and their abundance in the primary nucleotide databases is discussed.