The allochthonous microbiota in the proximal and distal intestine was investigated in three groups of Atlantic salmon (Salmo salar L.) fed a commercial diet and intraperitoneally injected with (a) phosphate-buffered saline (control), (b) lipopolysaccharide (LPS) from the fish pathogenic bacteria, Aeromonas salmonicida ssp. salmonicida, and (c) laminaran [β-(1,3)-d-glucan]. Denaturing gradient gel electrophoresis (DGGE) of the hyper variable V3 region was used to present the microbiota in different experimental groups. Sequencing and phylogenetic analysis of excised DGGE bands suggested that an intraperitoneal injection of LPS from A. salmonicida affects the allochthonous gut bacteria of Atlantic salmon to some extent, as Aeromonas enteropelogenes, Aeromonas veroni, Psychrobacter, Lactobacillus letvazi, Lactobacillus satsumensis, Pantoea, swine manure bacterium and several uncultured bacteria were unique for this group. On the other hand, the bacterial diversity of the allochthonous microbiota did not seem to be affected by injection of β-(1,3)-d-glucan. Sequences of this experimental group were most closely related to A. enteropelogenes, uncultured Escherichia and Lactobacillus aviarius ssp. aviarius.