In the present study the impact on autochthonous (adherent) bacteria in proximal intestine (PI) and distal intestine (DI) of Atlantic cod ( Gadus morhua L.) was evaluated following feeding of a control diet and a diet supplemented with 5% chitin. The autochthonous gut bacteria were investigated using denaturing gradient gel electrophoresis (DGGE). Analysis of the microbiota associated with PI and DI of Atlantic cod indicate that dietary chitin modulate the intestinal bacterial community. For example, band 25 ( Escherichia coli–like), band 14 ( Anaerorhabdus furcosa–like) and band 29 (uncultured bacterium–like) in PI were depressed by dietary chitin (P < 0.05). The number of bands (23.7 ± 5.4) in DI of fish fed chitin was marginally higher than the control fish (16.7 ± 2.1) (P = 0.065), and the relative abundances of band 6 (swine faecal bacterium–like) were marginally stimulated by dietary chitin (P = 0.095). Furthermore, the present study reports several novel sequences not previously reported in the gastrointestinal tract of Atlantic cod. Whether the dietary effect of chitin on gut bacterial community has any positive effect of fish health merits further investigations.