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In this study, we report ghrelin and leptin immunoreactive (ir) cells distribution in the gastrointestinal tract and blood ghrelin and leptin levels in rainbow trout (Oncorhynchus mykiss) and Murray cod (Maccullochella peelii peelii) fed diets with different fatty acid compositions. Juvenile rainbow trout and Murray cod were fed five iso-energetic experimental diets containing fish oil (FO) or one of the following vegetable oils (VO): olive oil (OO), sunflower oil (SO), linseed oil (LO), and palm oil (PO); as the added dietary lipid source. The presence and distribution of both ghrelin and leptin ir cells in the gastrointestinal tract were affected by the inclusion of VO. Ghrelin ir cells were found in the gastric glands of rainbow trout and in the mioenteric plexuses of the stomach of Murray cod fed FO. Ghrelin ir cells were localized in the mucosa of the intestine of rainbow trout and Murray cod fed VO. Leptin ir cells were more abundant in the epithelial lining of the mucosa folds and in the glands of the stomach of rainbow trout fed VO. Leptin immunoreactivity was detected in the gastric mioenteric plexus of Murray cod fed FO. No differences were found both in ghrelin and leptin levels in blood plasma or in the growth rates of rainbow trout and Murray cod fed the different experimental diets. These observations suggest that dietary fatty acids play a role in the peripheral feeding regulation.