As presently recognized, Herpetodiplostomum is a small genus of proterodiplostomid digeneans parasitic in crocodilians. Most members of Cheloniodiplostomum, a genus of proterodiplostomids that parasitize chelonians, were originally placed within Herpetodiplostomum. The 2 genera were distinguished based on the presence/absence of papillae on the holdfast organ and anterior extent of vitellarium. Our study of Herpetodiplostomum and Cheloniodiplostomum revealed a lack of consistent morphological differences between the genera. Therefore, we consider Cheloniodiplostomum to be a junior synonym of Herpetodiplostomum. Recent molecular phylogenetic studies included a number of proterodiplostomid taxa; however, DNA sequence data are not available for any Herpetodiplostomum or Cheloniodiplostomum species. Herein, we describe a new Herpetodiplostomum species from Geoffroy's side-necked turtle Phrynops geoffroanus from Mato Grosso State, Brazil. The new species can be distinguished from other Herpetodiplostomum species based on the distribution of vitellarium, level of development of holdfast papillae, and ratio of prosoma:opisthosoma width, among other characters. We provide the first molecular phylogeny of the Proterodiplostomidae that includes a Herpetodiplostomum species. The limited geographic distribution of Herpetodiplostomum spp. within the geographic ranges of caimans suggests a secondary host switching event from crocodilians to chelonian definitive hosts in the evolution of Herpetodiplostomum.