The effect of different feeding habits on gut morphology and digestive function has been intensively studied during the last decades but sympatric closely related fishes are relatively rare objects of such studies. In the present study, we have identified both morphological and physiological changes in the digestive system of a sympatric pair of whitefish represented by "normal" Coregonus lavaretus pidschian (benthivorous) and "dwarf" C. l. pravdinellus (planktivorous) forms. There were statistically significant differences in terms of histometric variables between segments of the stomach (height of lining epithelium, fold thickness and height values, and number of folds) and intestine (enterocyte height and fold height) within each form as well as between forms for the same segment of the digestive tract like in the stomach (height of lining epithelium and fold thickness) and intestine (enterocyte height, fold height and fold thickness). Both forms had a similar number (8-9 bands) and molecular weight of isoforms/isoenzymes of alkaline proteases inhibited by PMSF (serine proteases) based on zymogram analyses. The maximum level of activity of alkaline proteases, alkaline phosphatase, and aminopeptidase N were registered in the pyloric caeca for both forms. In contrast to these enzymes, the activity of α-amylase as well as of non-specific lipases and esterases in the pyloric caeca was similar or even lower if compared to other intestinal segments. In conclusion, both sympatric forms of whitefish showed some similarities in several of studied biochemical and histological parameters of their digestive tracts, regardless of their different feeding habits, which might be related to their genetical background.