Biodiversity research combines two dimensions, the horizontal one that contains species diversity, patterns among this diversity and its interconnections and the vertical one that deals with the history of biodiversity, i.e., its phylogeny. With these tight interconnections, the importance of so-called “lesser known groups” such as Nematomorpha and Gastrotricha can be shown. Two examples are the life cycle of Nematomorpha and the phylogenetic position of Gastrotricha. The life cycle of Nematomorpha is only partially known and almost no conclusions can be made about the impact of Nematomorpha on their hosts. For the phylogenetic position of Gastrotricha, alternative hypotheses are available, mainly due to different results of morphological and molecular (18S rDNA) analyses. It is demonstrated how these different hypotheses influence character interpretation and reconstruction among Protostomia (Gastroneuralia).