Technical Abstract: Complete replacement of fishmeal in feeds for carnivorous fishes often causes reduced growth and can negatively affect health. Salmonids fed diets containing full fat or defatted soybean meal develop dose dependent inflammation in the distal intestine (DI). Little is known about the sensitivity of different strains of rainbow trout to the effects of plant based diets. The current study investigated the response of a non-selected (NS) and selected (SE) strain of rainbow trout to a fishmeal free, plant based diet containing a high level of soybean meal. Fish from both strains were each divided into two groups and fed either a fish meal based control diet (FM) or an all plant meal diet (PM) containing 19% soybean meal, resulting in four treatments: FM-NS, FM-SE, PM-NS, and PM-SE. Tissue samples of the DI were collected after three months of feeding for histological (hematoxylin and eosin) and immunohistochemical (proliferating cell nuclear antigen, PCNA, and fatty acid binding protein 2, FABP2) analyses. Fish from the PM-NS treatment showed typical signs of DI inflammation, while the PM-SE did not and appeared equivalent to FM fed treatments. Moreover, the PM-NS fish displayed greater enterocyte PCNA staining indicating increased numbers of proliferating cells, and lower enterocyte Fabp2 staining compared to all other treatments. No differences were observed between FM-SE, FM-NS and PM-SE treatments. Results of the current work indicate that the sensitivity to dietary soybean meal varies between rainbow trout strains, and suggests that improved tolerance to dietary soy may be achieved by selective breeding.