Species of Corynosoma (Acanthocephala) are distributed worldwide as parasites of marine mammals and sea birds. Species diagnosis is based on morphological characters, including the size and number of hooks in the proboscis and the number of spines in the dorsal and ventral regions of the body. We inferred the phylogenetic relationships of 10 nominal species of Corynosoma through analysis of internal transcribed spacers (ITS-1, ITS-2) and 5.8S ribosomal RNA sequences. Nucleotide distances between species of Corynosoma ranged from 0.4 to 11% for ITS sequences. Maximum parsimony and likelihood analyses indicated that species of Corynosoma that inhabit hosts in the marine environment form a monophyletic assemblage, but yielded conflicting hypotheses for the relationship of Corynosoma cetaceum to other members of the genus. However, parsimony and likelihood analyses were consistent for many Corynosoma sister species relationships of (e.g., C. australe plus C. bullosum, C. validum plus C. villosum, C. caspicum plus C. magdaleni, and C. enhydri plus C. strumosum). This phylogenetic framework was used to evaluate taxonomic controversies concerning C. cetaceum and C. caspicum.