AbstractMany marine bivalves have complex life histories with distinct developmental processes and genetic mechanisms. Larval development for most bivalves is often a prolonged and crucial physiological stage, where they suffer mass mortality due to early-acting genetic load. In this study, we describe genetic changes taking place within a single generation of families of the Mediterranean musselMytilus galloprovincialisover 23 days of larval development. Using replicated cultures and a pooled sequencing approach, we demonstrate that temporal balancing selection at the majority of loci preserve genetic variation in the early developmental stages ofM. galloprovincialis. Balancing selection may be the mechanism which maintains standing genetic variation within the mussel genome and may improve the chances of survival and shield larvae from high levels of genetic load. Additionally, we used changes in allele frequencies to identify potential size-associated SNPs and viability-associated SNPs and found that patterns of genetic changes in directionally selected SNPs cannot be simply explained by traditional theories of genetic purging or directional selection without consideration of balancing selection. Finally, we observed a negative correlation between larval growth rates and survival, implying a potential trade-off relationship between the 2 commercially relevant phenotypes.