Modern morphology-based systematics, including questions of incongruence with molecular data, emphasizes analysis over similarity criteria to assess homology. Yet detailed examination of a few key characters, using new tools and processes such as computerized, three-dimensional ultrastructural reconstruction of cell complexes, can resolve apparent incongruence by re-examining primary homologies. In nematodes of Tylenchomorpha, a parasitic feeding phenotype is thus reconciled with immediate freeliving outgroups. Closer inspection of morphology reveals phenotypes congruent with molecular-based phylogeny and points to a new locus of homology in mouthparts. In nematode models, the study of individually homologous cells reveals a conserved modality of evolution among dissimilar feeding apparati adapted to divergent lifestyles. Conservatism of cellular components, consistent with that of other body systems, allows meaningful comparative morphology in difficult groups of microscopic organisms. The advent of phylogenomics is synergistic with morphology in systematics, providing an honest test of homology in the evolution of phenotype.Keywords: Caenorhabditis elegans; comparative morphology; evolution of novelty; congruence; plant parasitism; systematics . We contend that upon closer examination, superficial incongruence, or incongruence of morphology owing to inadequate character conceptualization, can be resolved. To understand the patterns and process of phenotypic evolution, such as that of parasitism, it is essential to explicitly dissect homologies of key adaptive characters. We present an example of a programme to resolve character evolution, herein between apparently disparate free-living and parasitic taxa, by addressing homology at finer scales of morphology. We propose that complexity of similarity for guiding homology proposals can be discovered at a cellular level, using precise tools such as computerized ultrastructural reconstruction. These tools can also more explicitly reject presumed homologies that are incongruent with robust molecular phylogenies.