Settlement and metamorphosis mark a critical transition in the life cycle of marine invertebrates, during which larvae undergo substantial morphological, sensory, and genetic changes. High mortality during or after metamorphosis is commonly observed in both wild and hatchery settings, however, the underlying causes of this mortality remain poorly understood. Previous pair-crossing experiments with the Pacific oyster, Crassostrea gigas showed that substantial genotype-dependent mortality (GDM) occurs around metamorphosis, but, owing to sparse temporal sampling, it remains unknown whether mortality occurs just before, during, or after settlement. In this laboratory study, microsatellite marker segregation ratios were followed daily throughout the settlement and metamorphosis of an inbred, F2 cross of the Pacific oyster to examine the fine-scale patterns of GDM in larvae and spat. Genetic control of settlement timing was also examined using a quantitative trait locus (QTL) mapping approach. Settlement occurred over nine days (day 18 to day 27 post-fertilization) with 68% of individuals settling on an early (day 19) and a late (day 24) time point. Tracking the survival of spat for 40 days after initial settlement revealed almost no post-settlement mortality. Temporal analysis revealed that three of 11 loci exhibited segregation distortion at metamorphosis, one of which (Cg205) was followed throughout settlement. Alternative temporal patterns of selection against each homozygote at Cg205 suggest possible defects in both the competency pathway (inability to initiate metamorphosis) and the morphogenesis pathway (mortality during the metamorphic transition). QTL mapping of settlement timing identified three individual and one epistatic QTL (29% of the variance explained), however, two of these loci were closely linked to markers exhibiting GDM at metamorphosis, thus making it difficult to distinguish between genetic variance in settlement timing and differential mortality early or late in settlement. Overall, results from this study highlight the complex temporal patterns of viability selection during metamorphosis and show that endogenous mortality during the larval-juvenile transition appears to be focused during or just prior to metamorphosis. Fine-scale experimental analysis of settlement can reveal important genetic insights into larval settlement behavior and the sources of larval mortality, and future studies should be able to further dissect the functional targets of selection during metamorphosis.