A model organism in developmental biology is defined by its experimental amenability as well as by resources created for the model system by the scientific community. For the most powerful models, the combination of both has already yielded a thorough understanding of development. However, the number of developmental model systems is still limited, and their phylogenetic distribution is heavily biased. Members of one of the largest animal phylum, the mollusks, for example, have long been neglected as developmental model organisms. To remedy this shortcoming, we produced a detailed developmental transcriptome for the bivalve mollusk Mytilus galloprovincialis. Our high-quality transcriptome allowed us to identify transcriptomic signature of developmental transitions and perform a first comparison with Crassostrea gigas that could further be applied for multi-species comparisons. To allow co-labelling studies, we optimized protocols for immunohistochemistry and hybridization chain reaction and combined both techniques to obtain high-resolution co-expression maps of developmental genes. The resources and protocols we describe here thus represent an enormous boost for the establishment of the Mediterranean mussel as a laboratory model in developmental biology.