Variation in growth and survival of planktonic larvae has profound effects on marine population abundance. Environmental causes of differential larval growth and mortality are well studied, but genetic variation in these traits is less well understood. Here, we reveal genetic variation in survival and growth of full-sib larvae of the Pacific oyster Crassostrea gigas reared under identical conditions. We size-selected 1.42 million, 24 d old larvae to produce small, medium, and large size classes, constituting 93% of the population. Parental tissues and a total of 144 larvae sampled from each size class were individually genotyped with a panel of 45 mapped DNA markers. Consistent with previous work, 11 markers had genotypic frequencies that differed significantly from their Mendelian expectations and, upon mapping, are explained by 6 viability quantitative trait loci (vQTL). Notably, shell-length variance among size classes maps to 6 major growth QTL (gQTL), with just 2 collectively explaining 18% of the variance. We found little overlap between vQTL and gQTL, suggesting that variation in these larval traits is controlled by different genes. This study demonstrates the feasibility of genotyping single larvae for the identification of multiple QTL. Understanding genetic variation in larval biology is important for a comprehensive understanding of marine recruitment.