Comparative analyses of different regions of ribosomal DNA have become a popular tool in understanding the relationship among different species and genera and nematodes are no exception to this. In this study, molecular relationships were inferred from a nearly complete small subunit (SSU) of total 16 OTUs for five species of Mylonchulus, Paramylonchulus and Pakmylonchulus collected from various parts of Japan with two out-group taxa (Mononchus aquaticus and Clarkus papillatus) to examine the relationship among these species. Out of 1685 bp SSU rDNA sequences, phylogenetic trees using distance (NJ), parsimony and likelihood algorithms were performed. Obtained tree topologies were stable across algorithms and sequence data show that populations of the same species clustered together and four out of five species (M. brachyuris, M. hawaiiensis, M. oceanicus, M. sigmaturus) formed a monophyletic assemblage while M. mulveyi formed a sister group. Populations of species lacking subventral teeth but with a double gonad (M. oceanicus) stand with other Mylonchulus species, thereby confirming the synonymy of Pakmylonchulus, while populations with a narrow buccal cavity with few rows of denticles, no subventral teeth and a single prodelphic gonad (M. mulveyi = Paramylonchulus mulveyi) support to some extent the validity of the genus Paramylonchulus. Though a preliminary investigation, it is the first report on molecular relationships in Mylonchulus, probably a paraphyletic genus. Our results suggest that SSU rDNA sequence data are useful in understanding the relationship between genera and species.