The most promising novel approaches to managing nematode pests are through understanding and exploiting genomic and molecular aspects of pathogenesis, survival strategies and reproduction. Efficient progress, however, requires comprehensive and resolved phylogenies, and particularly so in the order Tylenchida , that includes most agricultural pests. The practical need for a phylogenetic framework is rooted in the heterogeneity of Tylenchida’s more than 2000 described species and the nearly 400 species of Aphelenchida. Tylenchida hosts include invertebrates, fungi and plants; plant parasitic strategies include migratory ectoparasitism, burrowing endoparasitism, and sedentary ecto- and endoparasitism; some strategies are associated with little apparent impact on host cells and others induce profound host transformations. Based on a few species, early evidence is that whereas some genes involved in parasitism are conserved, others are specialized between putative “close relatives” and even between species of a particular genus. Preliminary phylogenies suggest that feeding strategies within Tylenchida are highly convergent; for example sedentary endoparasitism with host cell transformations apparently has arisen at least six times, and we cannot assume that the mechanisms and genes behind these separate systems are congruent ---or that knowledge of one system provides a basis to predict or understand another. Although presently it is not realistic to unravel the genomics of every plant parasite, it is feasible to decipher underlying mechanisms of patterns of pathogenesis, survival strategies and reproduction through tylenchid-model systems. However, rational and efficient selection of, and prediction from, such models requires the framework of a comprehensive, reliable and highly resolved phylogeny of Tylenchida. For example, preliminary trees based on SSU rRNA support both root knot (Meloidogyne) and cyst (Heteroderidae) nematodes as monophyletic but reject the widely held view that these two groups of sedentary endoparasites collectively are closely related and that mechanisms and genes of parasitism are necessarily shared. An alternate hypothesis that Heteroderidae share a clade with Hoplolaimidae (largely but not exclusively migratory ectoparasites) suggests new models that recognize diversity and a basis for potentially informative genetic (with respect to parasitism genomics) comparison. Beyond cyst nematodes, phylogenetic resolution is basic to efficiently extending the growing understanding of parasitism mechanisms and genomics to the diverse range of sedentary and migratory tylenchid parasites of major agricultural importance. Recent initiatives toward a “deep level” phylogenetic overview of Nematoda provide a unique “window of opportunity” that can be leveraged to efficiently, rapidly, and cost-effectively develop a much-needed highly-resolved tylenchid phylogeny within this broader scheme.