Both insect parasitic/entomopathogenic nematodes and plant parasitic nematodes are of great economic importance. Insect parasitic/entomopathogenic nematodes provide an environmentally safe and effective method to control numerous insect pests worldwide. Alternatively, plant parasitic nematodes cause billions of dollars in crop loss worldwide. Because of these impacts, it is important to understand how these nematodes evolve, and, in the case of entomopathogenic nematodes, how their bacterial symbionts evolve. This dissertation contains six chapters. Chapter one is a review of DNA markers and their use in the phylogenetic systematics of entomopathogenic and insect-parasitic nematodes as well as a review of phylogenetic, co-phylogenetic, and population genetic methodologies. Chapter two characterizes positive destabilizing selection on the luxA gene of bioluminescent bacteria. Our data suggests that bacterial ecology and environmental osmolarity are likely driving the evolution of the luxA gene in bioluminescent bacteria. Chapter 3 examines relationships among bacteria within the genus Photorhabdus. Our analyses produced the most robust phylogenetic hypothesis to date for the genus Photorhabdus. Additionally, we show that glnA is particularly useful in resolving specific and intra-specific relationships poorly resolved in other studies. We conclude that P. asymbiotica is the sister group to P. luminescens and that the new strains HIT and JUN should be given a new group designation within P. asymbiotica. Chapter 4 characterizes the morphology of the head and feeding apparatus of fungal feeding and insect infective female morphs of the nematode Deladenus siricidicola using scanning electron microscopy. Results showed dramatic differences in head, face, and stylet morphology between the two D. siricidicola female morphs that were not detected in previous studies using only light microscopy. Chapter five utilizes comparative transciptomics to identify putative plant and insect parasitism genes in the nematode Deladenus siricidicola. Results from this study provide the first transcriptomic characterization for the nematode Deladenus siricidicola and for an insect parasitic member of the nematode infraorder Tylenchomorpha. Additionally, numerous plant parasitism gene homologues were discovered in both D. siricidicola libraries suggesting that this nematode has co-opted these plant parasitism genes for other functions. Chapter six utilizes a phylogenomic approach to estimate the phylogeny of the nematode infraorder Tylenchomorpha.