The systematic relationships of aspinose allocreadiid-like digeneans from Middle-American and Neotropical freshwater fishes, such as Wallinia Pearse, 1920, Margotrema Lamothe-Argumedo, 1970, Magnivitellinum Kloss, 1966 and other related genera, remain enigmatic. Wallinia (2 spp.) and Margotrema (2 spp.) have been placed in the subfamily Walliniinae, within the Macroderoididae. Recent descriptions of species in these genera have followed this classification but have raised questions about their affinities with macroderoidids. Partial sequences of the 28S rRNA gene of Wallinia chavarriae Choudhury, Hartvigsen & Brooks, 2002 and Margotrema bravoae Lamothe Argumedo, 1970, as representatives of their genera, were used in a phylogenetic analysis along with the available sequences of macroderoidids and allocreadiids. Results from Maximum Parsimony, Maximum Likelihood and Bayesian Analyses were identical in placing both genera into one clade along with allocreadiids rather than the macroderoidids. Margotrema was the sister group of Crepidostomum Braun, 1900, and Wallinia was the sister group of both Margotrema and Crepidostomum combined. Bootstrap and Bremer values, as well as posterior probabilities derived from Bayesian analysis strongly supported these relationships in three analyses.