The Precambrian–Cambrian interval saw the first appearance of disparate modern metazoan phyla equipped with a wide array of mineralized exo- and endo-skeletons. However, the current knowledge of this remarkable metazoan skeletonization bio-event and its environmental interactions is limited because uncertainties have persisted in determining the mineralogy, microstructure, and hierarchical complexity of these earliest animal skeletons. This study characterizes in detail a previously poorly understood fibrous microstructure—the lamello-fibrillar (LF) nacre—in early Cambrian mollusk and hyolith shells and compares it with shell microstructures in modern counterparts (coleoid cuttlebones and serpulid tubes). This comparative study highlights key differences in the LF nacre amongst different lophotrochozoan groups in terms of mineralogical compositions and architectural organization of crystals. The results demonstrate that the LF nacre is a microstructural motif confined to the Mollusca. This study demonstrates that similar fibrous microstructure in Cambrian mollusks and hyoliths actually represent a primitive type of prismatic microstructure constituted of calcitic prisms. Revision of these fibrous microstructures in Cambrian fossils demonstrates that calcitic shells are prevalent in the so-called aragonite sea of the earliest Cambrian. This has important implications for understanding the relationship between seawater chemistry and skeletal mineralogy at the time when skeletons were first acquired by early lophotrochozoan biomineralizers.