In an effort to identify potential probionts, four bacterial strains obtained from the intestinal tract of wild‐caught Atlantic cod, Gadus morhua, were tested for their antagonistic activity against Vibrio anguillarum and Aeromonas salmonicida, two of the most common bacterial pathogens in cod aquaculture, using a well‐diffusion agar assay at two incubation temperatures: 13 and 20 °C. The tested bacteria exhibited dissimilarity in their inhibitory action against the target pathogens – an enhanced activity was particularly observed for strains GP11 and GS11 at the highest incubation temperature. Based on the 16S ribosomal DNA gene sequence analysis, the strains showed high similarity to Psychrobacter sp. (strain GP11), Shewanella sp. (GS11), Photobacterium sp. (GP31) and Vibrio sp. (GV11). The incubation of Atlantic cod head kidney cells with the heat‐inactivated probiotic strains resulted in the differential expression of immune‐response genes that are related to bacterial defence and inflammation. Thus, the gut‐derived bacterial strains have probiotic potential and their possible immunomodulatory capabilities could be determined under in vitro conditions.