Oysters, like many marine bivalves, are characterized by very high fecundity and low survival rate at early stages of life. Rearing conditions in hatcheries (i.e. density, feeding, temperature...) are different from those observed in the wild. Additionally, slow growing larvae are culled by sieving. As previous studies have shown that genetic variability exists for several early development traits, we aimed to assess if common hatchery rearing practices exert specific selective processes at the larval stage. In order to avoid possible bias and to increase the number of families studied, we used a mixed-family approach with subsequent parentage analysis using a recently developed set of three multiplexed microsatellite markers. We studied the variance in reproductive success of controlled factorial crosses in order (1) to evaluate the effect of intensive rearing practices on effective population size (estimating the genetic effect of discarding the smallest larvae and/or the slowest to reach metamorphosis), (2) to describe the temporal genetic structure of the larval population and (3) to observe possible genotype x environment interaction effects on larval growth and survival. Our results confirm the existence of genetic variability for several early development traits. We conclude that the combined effects of culling and high temperature can lead to significant selection at the larval stage.