The effects of four prebiotics (fructo-oligosaccharide, Bio-MOS®, transgalacto-oligosaccharide and GroBiotic®-A) on digestive enzymes and intestinal morphology were studied in juvenile hybrid striped bass (Morone chrysops×M. saxatilis) and red drum (Sciaenops ocellatus) using two separate 8-week feeding trials. Red drum were fed experimental diets with the four prebiotics each individually supplemented at 1 % and hybrid striped bass were fed diets supplemented with GroBiotic®-A at 1 and 2 %. Both trials were conducted with each diet fed to apparent satiation twice per d to three replicate groups of fifteen juvenile fish. For histomorphological analysis, gastrointestinal tract (GIT) samples from three randomly selected fish per tank were taken at 4 and 8 weeks for hybrid striped bass and at 8 weeks for red drum. For both trials, GIT samples from two randomly selected fish per tank were taken at 4 and 8 weeks and analysed for pepsin, trypsin, chymotrypsin, aminopeptidase, α-amylase, lipase, and both acid and alkaline phosphatase activities. The results of the histological evaluation indicated that the inclusion of prebiotics was adequate to elicit structural changes in the GIT of both species. On the other hand, no significant changes in the enzyme activities were detected at week 8 in both species. However, there was a transient effect of Bio-MOS® supplementation on the activities of aminopeptidase, α-amylase and alkaline phosphatase at week 4 in red drum only. Thus, previously observed improvements in nutrient digestibility by these fish in response to prebiotic supplementation appear to be mostly related to changes in GIT structure as opposed to the enhancement of digestive enzyme activity.