The evolutionary relationships among the six nominal genera within the spinicaudate clam shrimp family Limnadiidae, as well as the validity of the limnadiid genus Eulimnadia, have been much debated in the literature with little consensus emerging. The lack of resolution on these topics impedes evaluations of limnadiid biodiversity, phylogeny, and character evolution. To address these issues, we used Bayesian and parsimony methods to analyze DNA sequences from three genetic loci (28S, 12S, cytb) that were obtained from representatives of five nominal limnadiid genera and one undescribed limnadiid species. These analyses confirm the monophyly of Eulimnadia and the most taxonomically inclusive phylogenetic analysis (28S) produces the following tree topology: (((((Eulimnadia, Metalimnadia), undescribed limnadiid), Imnadia), Limnadopsis), Limnadia). This topology is inconsistent with prior estimates of limnadiid inter-generic relationships. Maximum likelihood-based constraint analyses demonstrate that the above topology is significantly better than prior hypotheses of limnadiid relationships, and support the monophyly of Eulimnadia. Morphological character optimization on this topology suggests that the postulated close relationship between Limnadia and Eulimnadia is based on shared ancestral characteristics rather than synapomorphies. Furthermore, the discovery of the genetically distinct undescribed limnadiid lineage strongly supports the necessity of efforts to better evaluate limnadiid biodiversity, especially those in poorly collected zoogeographic regions.