Molluscan larval ontogeny is a highly conserved process comprising three principal developmental stages; trochophore, veliger and metamorphosis into the juvenile. A characteristic that is unique to each of these stages is shell design, termed prodissoconch I, prodissoconch II and dissoconch in bivalves. These shells vary in morphology, mineralogy and microstructure. The discrete temporal transitions in shell biomineralization between these larval stages are utilized in this study to investigate transcriptional involvement in several distinct biomineralization events. Scanning electron microscopy and X-ray diffraction analysis of P. maxima larvae and juveniles collected throughout post-embryonic ontogenesis, document the mineralogy and microstructure of each shelled stage as well as establishing a timeline for transitions in biomineralization. P. maxima larval samples most representative of these biomineralization distinctions and transitions were analyzed for differential gene expression with the microarray platform PmaxArray 1.0. A number of known shell matrix genes and novel transcripts are reported as differentially expressed in correlation to the mineralization events of P. maxima larval ontogeny. However, only a single transcript, PM066, was noted as being expressed before and after the transition to the adult shell design. No other known/putative adult shell matrix genes from P. maxima were detected in association with the larval shells prodissococh I and II suggesting that there expression is either below detection limits or an almost entirely different sets of genes are potentially responsible for larval and adult shell mineralization. This interdisciplinary investigation has linked the shell developments of P. maxima larval ontogeny with corresponding gene expression profiles, furthering the elucidation of bivalve development and shell biomineralization.