The effects of partial (75%; diet PP75) and total (100%; diet PP100) replacement of fish meal by plant protein sources on the intestinal nutrient absorption of gilthead sea bream and rainbow trout were examined over a 12-week growth trial. The diets comprised a mixture of plant ingredients (corn gluten meal, wheat gluten, extruded peas and rapeseed meal) and met the amino acid requirements of the fish. A third group of fish on a fish meal diet was used as a control for comparative purposes. Diets were tested in triplicate and fish were fed twice a day until visual satiation. At the end of the trial, we measured amino acid (L-leucine, L-lysine, L-phenylalanine, Lalanine and L-proline) and D-glucose absorption at short term (6 h) and long-term (36 h and 48 h in rainbow trout and sea bream respectively) post-feeding by means of brush border membrane vesicles obtained from pyloric caeca, proximal intestine and distal intestine. The absorption pattern at 6 h post-feeding was modified in both species in response to fish meal replacement. In PP75-fed trout absorption was delayed from pyloric caeca to proximal and/or distal intestinal segments, thus total absorption capacity was maintained in this group. On the contrary, total uptake was significantly decreased in trout fed the PP100 diet and in sea bream on both PP75 and PP100 diets. Glucose transport capacity was increased in both experimental sea bream groups and in PP75 trout. Long-term transport capacity was up-regulated for both species. Our results show that intestinal nutrient absorption is modified in response to the use of high levels of plant protein sources and that these changes are species-specific.