This dissertation presents the first phylogenetic hypotheses for the nemertean clade Pilidiophora obtained using modern phylogenetic methods. These methods include parsimony analysis and Bayesian inference on character data from several sources, including DNA sequences for three genes, morphological characters from living specimens and histological sections, and developmental character data.

Morphological characters traditionally used by nemertean taxonomists to build classifications are examined with parsimony analysis in chapter two. This analysis includes 107 characters coded from 66 species. Several characters, which were traditionally considered useful for taxonomic purposes, are demonstrated to be homoplastic and misleading for pilidiophoran taxonomy. Additional characters are suggested to facilitate future phylogenetic and taxonomic works.

Chapter three examines DNA sequences for three genes, cytochrome oxidase subunit 1, 16s ribosomal DNA and 28s ribosomal DNA, both individually and in combination with other data sets in a parsimony and Bayesian inferences analyses. Conflict between data partitions was examined using the incongruence length difference test and partition analysis of bootstrap alteration (PABA). The ILD test demonstrated that there is significant incongruence between data partitions. However, PABA analysis indicates greater phylogenetic resolution is achieved when data partitions are analyzed simultaneously.

Results from chapters two and three support several well supported clades in terms of synapomorphies. Clades of the genera Baseodiscus, Evelineus , and Notospermus species are reliably recovered in most data partitions. However, the three heteronemertean mega-genera, Cerebratulus, Lineus and Micrura, are polyphyletic. Chapter four is a revision of genera and species that are well defined in the phylogenies of chapter two and three.

Pilidiophorans are known for their stereotypical indirect developing, planktotrophic larvae, pilidia. However, several different morphotypes are known and include a few encapsulated forms. Here several new morphotypes are described using light and confocal microscopy. Several hypotheses of larval characters and life-history evolution are tested for correlations. Although no correlations were found, it appears that an encapsulated type of pilidium evolved four times.