Tommotiids are distinctive components of the early Cambrian small shelly fauna, almost invariably represented by isolated phosphatic sclerites derived from a multielement protective cover (scleritome). The unusual range of tommotiid sclerite morphologies and unknown construction of the scleritome have severely hampered our understanding of their phylogenetic affinities. However, recent description of rare, articulated scleritome material belonging to the tommotiid genera Eccentrotheca and Paterimitra support the hypothesis that some tommotiids fall within the stem group of the lophophorate phyla Phoronida and Brachiopoda and that at least some tommotiid sclerites are homologous precursors of the shells of organophosphatic brachiopods. Here we show that the shell microstructure of Eccentrotheca and Paterimitra share substantial similarities with paterinid brachiopods. While paterinids possess an overall brachiopod morphology, their microstructure appears more similar to Eccentrotheca and Paterimitra than to nonpaterinate lingulids. These findings strongly support the existence of a brachiopod total group that is solidly rooted within tommotiids, and identify the organophosphatic skeletal composition as plesiomorphic with calcareous shells as derived. The microstructural changes of the proposed tommotiid-brachiopod transition probably reflect an adaptation to fluctuating food and phosphorous intake that came with the switch to a sessile life style at the base of the tommotlid clade.