Technical Abstract: Microsatellite DNA markers were used to determine the pedigree of the top 1% and of the bottom 1% of progeny in a large scale commercial growth trial of 24,000 rainbow trout (Oncorhynchus mykiss)from 20 full-sib families (20 dams x 10 sires in a nested mating design). The progeny were pooled at eyed stage and divided into 2 groups. Half of the fish from each family were fed a standard fishmeal-based diet and the other half were fed a plant protein based diet to determine the relative family rankings in each case and calculate genotype by feed interactions. Large genetic variation for growth was identified for both diets and the sire effect was found to be highly significant. The family rankings were very similar for both diets, which suggest that the fish that grow faster on fishmeal diet are likely to grow faster on plant-based diets, and therefore current commercial strains that exhibit superior growth should retain their improved performance if raised on plant-based diets. Additionally, we determined that although microsatellites can be used for accurate parentage assignment in a large scale selection program, a more rapid, universal and cost-effective procedure should be developed.