The blue mussel, Mytilus edulis, plays important roles as both a keystone and aquaculture species across the globe. Although many studies have focused on understanding mussel development for ecological and hatchery-related purposes, surprisingly little is known about the molecular changes that underlie mussel ontogeny. To obtain a comprehensive view of these molecular patterns, we collected hatchery samples in various stages of development (egg, sperm, trochophore, veliger, pediveliger, postlarva, and adult), co-extracted RNA and DNA, and sequenced each of these samples using RNA-seq and whole genome bisulfite sequencing (WGBS), respectively. Gene expression analyses revealed strong stage-specific clustering patterns (Fig. 1A) and large numbers of differentially expressed genes between developmental transitions (e.g., pediveliger to postlarva; Fig. 1B), indicating extensive differences in gene expression profiles across stages. In addition, a large set of genes exhibiting stage-specific expression were identified. Similarly, differential DNA methylation analyses revealed many differentially methylated loci throughout the genome when contrasting stages spanning developmental transitions, as well as several loci that exhibited stage-specific methylation. These results significantly advance our understanding of blue mussel development and provide valuable novel genomic resources for aquaculturists and scientists alike.