Morphological and molecular studies were used to determine the systematic affinity of the sea urchin parasite, Echinomermella matsi. The absence of somatic ornamentation and external openings in the parasitic juveniles and adults, aside from a small non-functional mouth and male reproductive opening, shows a striking degree of morphological reduction in Echinomermella as an adaptation to a parasitic life style. A phylogenetic analysis of E. matsi by the maximum likelihood (ML) and neighbour-joining (NJ) methods places it within the Order Enoplida. This indicates that Echinomermella evolved from free-living marine enoplids and is not closely related to the Mermithidae as previously thought. The absence of a vulva and male genital supplements, coupled with the modified spicule tips, suggest that traumatic insemination is the standard method of mating. The morphological modifications in Echinomermella indicate a long period of co-evolution with sea urchins, possibly extending back to the Palaeozoic.