The composition of the gut microflora of Atlantic salmon is dependent on the environmental conditions such as water temperature and diet. Our recent studies indicate that these bacteria reach their minimum level during the warmer period of the year where opportunistic pathogens such as Vibrios overgrow. Lactic acid bacteria (LAB) have been shown to confer many health benefits to the health of fish including exclusion and displacement of pathogenic bacteria in the gut and production of bacteriocins. In this study we isolated and characterised a total of 160 LAB strains from the hindgut of Atlantic salmon from two commercial fish farms and fed either two different diets (farm 1) or four trial diets (farm 2). These strains were sequenced using 16S rRNA gene universal primers and typed using the PhPlate-LB system. The LAB strains belonged to nine species of which Enterococcus, Pediococcus and Weissella species accounted for 49.4% of the total population. Strains found in more than one sampling occasion or in more than one diet were further tested for production of bacteriocin, their adhesion capabilities and potential cytotoxicity to fish cell line ASK. Most of the strains showed low adhesitivity ranging from 2 to 10 CFU/cell) with some strains being also cytotoxic to ASK cells. However, certain strains belonging to E. casseliflavus and W. hellenica showed a high adhesion (19 and 21 CFU/cell respectively). These strains did not produce any cytoxic effect on this fish cell line. Bacteriocin production varied among the strains and their inhibition effect was strain specific. The importance of these strains as probiotic candidates will be discussed.