Oligacanthorhynchus (Rudolphi, 1819) Schmidt, 1972 (Oligacanthorhynchidae) is a typical parasite of opossums (Didelphidae). This species of acanthocephalan exhibits a wide distributional range that extends from Brazil to as far north as the United States, but no data on the genetic divergence of this helminth has been provided thus far along its entire geographic range. The facts that O. microcephalus shows a relatively wide geographic range in Mexico and that it has been recorded in 3 species of opossum allowed us to conduct a molecular prospecting study to assess the genetic divergence among individuals and populations as well as to detect potentially exclusive lineages indicative of the presence of a species complex. In total, 81 specimens identified as O. microcephalus were collected from the intestines of 3 species of opossum in 8 localities across central and southeastern Mexico. The DNA sequences of 2 genes were generated; cytochrome c oxidase subunit 1 (cox 1) of the mitochondrial DNA and the domains D2 and D3 from large subunit of the nuclear ribosomal RNA (LSU). Maximum parsimony, maximum likelihood, and Bayesian inference analyses were performed for each dataset alone and for the combined datasets (LSU cox 1). All the phylogenetic analyses yielded 3 major clades with high bootstrap and posterior probability support values and with relatively high genetic divergence levels for both markers. However, the morphological study of specimens through both light and scanning electron microscopy, as well as the morphometric data, indicate that those specimens allocated into Clade I are smaller than those contained in Clades II and III. Lower genetic divergence values, as well as no clear-cut morphometric differences, indicate that Clades II and III are likely not independent lineages. Our results show at least 2 genetic lineages that may represent independent species, but we refrain at the moment on describing a new species in the lack of evidence gathered from a wider geographic range.