Evidence is presented in support of the following phylogenetic hypotheses: (1) Sipuncula are the sister taxon of Mollusca; (2) the two aplacophoran taxa, Neomeniomorpha (= neomenioids) and Chaetodermomorpha (= chaetoderms), are monophyletic with a common neomenioid-like ancestor, and of the two taxa, Chaetodermomorpha are more derived; (3) Aplacophora and Polyplacophora are sister taxa and form a clade, Aculifera; (4) Aculifera are the sister group of the remaining extant mollusks, Conchifera; and (5) Aplacophora are progenetic Aculifera. The evidence is based on homologies of early and late embryological development, adult morphologies, and molecular analyses. Embryological development in sipunculans and mollusks shows a close relationship between them, and embryological development of the shell separates Aculifera and Conchifera. Adult morphologies indicate: (1) monophyly of Aplacophora; (2) sister-group relationship between Aplacophora and Polyplacophora; (3) a molluscan plesiomorphy of nonsegmented serial replication of organs; and (4) progenesis in Aplacophora. Molecular evidence supports the embryological and morphological relationships between Sipuncula and Mollusca. Mollusca are thus hypothesized to be coelomate Eutrochozoa, which share an ancestor that probably had serial replication of organs. Differences in size and structure of the coelom among Eutrochozoa are hypothesized to have been brought about by changes in the timing and the process of cavitation of the mesodermal bands that arise from cell 4d. Through the process of progenesis Aplacophora retained an ovoid embryological shape and several internal structures that, although they appear to be in a primitive state, are actually secondarily derived as is quadrant D specification during early cleavage.