A hierarchical breeding design was used to determine if winter flounder Pseudopleuronectes americanus embryos and yolk-sac larvae sired by Georges Bank males developed and grew larger than fish sired by Passamaquoddy Bay males, and to examine parental contributions to variations in fertilization success, time to 50% hatch, hatch success and larval morphological development. Significant stock effects were detected for time to hatch and larval development. Eggs fertilized by Passamaquoddy Bay males reached 50% hatch significantly earlier than eggs fertilized by Georges Bank males. Larvae sired by Georges Bank males were significantly larger during larval development for four of the six traits measured at 12 days post-hatch: head depth, jaw length, myotome height and body area. Embryo and larval development were strongly influenced by maternal contributions; there were significant maternal variance components for the majority of the variables measured. Paternal variance components were significant for fertilization success, time to hatch, larval jaw length and larval head depth, however, they acted principally through parental interactions. This information has important implications for the long-term sustainable development of winter flounder for aquaculture purposes as well as for understanding winter flounder genetic variation in the wild.