The primary aim of the present study was to evaluate the population level of adherent (autochthonous) aerobic and facultative anaerobic bacteria in the hindgut of healthy Arctic charr (Salvelinus alpinus L.) fed dextrin or inulin. This was assessed by the dilution plate technique, and visualized using both transmission and scanning electron microscopy. A population level of 4.8 × 105 adherent bacteria per gram wet mass was found in the hindgut of fish fed a casein-based diet supplemented with 15% dextrin. However, substituting dextrin with 15% inulin reduced the bacterial population level in the hindgut (3.56 × 104). A total of 217 bacterial isolates were identified by key phenotypical and biochemical characteristics. In addition, 22 strains were also identified by partial sequencing of the 16S rRNA gene. The composition of bacteria colonizing the hindgut of Arctic charr fed dextrin was dominated by the genera Staphylococcus, Pseudomonas, Micrococcus, Psychrobacter glacincola and Streptococcus. However, bacteria colonizing the hindgut of fish fed inulin were dominated by Gram-positive bacteria of the genera Staphylococcus, Streptococcus, Carnobacterium and Bacillus. While Carnobacterium divergens-like strains were isolated from charr fed dextrin, Carnobacterium maltaromicus-like strains were isolated from the hindgut of fish fed inulin. Electron microscopical analysis of hindgut regions confirmed traditional culture-based microbial analysis as fewer bacterial cells were observed between microvilli and associated with the surfaces of enterocytes of fish fed inulin rather than dextrin.