Ocean acidification (OA) adversely impacts initial shell formation of bivalve larvae. Despite many studies observing large differences in developmental success between distinct genetic populations of bivalves exposed to OA, few studies have investigated the molecular mechanisms that enable resilient larvae to build their initial shell. This knowledge is key to their ecological and economical conservation. Herein, we used a genetic-selection program for Crassostrea gigas to produce a resilient and susceptible larval lineage to OA. The resilient and susceptible larvae were sampled every 3-hours over a 24-hour period in OA and control conditions. The susceptible lineage failed to develop a larval shell in OA conditions, whereas 52 % of the resilient lineage developed to D-larvae by 24 hours post fertilisation. We measured the expression of 23 genes involved in initial shell formation by RTqPCR, which revealed significant genotype-by-time and environment-by-time interactions for the transcription of these genes. OA upregulated a single gene encoding a protein involved in ion transport, Na+ K+ ATPase, in both the resilient and susceptible lineage. These results were corroborated by a second experiment involving 25 pair-mated C. gigas families exposed to OA and control conditions. Our findings indicate C. gigas have a fixed capacity to modulate expression of genes involved in initial shell formation in response to OA. Thus, phenotypic differences to OA between the resilient and susceptible lineage are likely explained by other cellular processes, such as bioenergetics or protein translation.