Atlantic salmon farming is Australia’s most rapidly growing aquaculture industry which is based in Tasmania. During the production cycle, salmon experience a variety of health issues including bacterial infections which occur more often during the warmer summer months, when temperatures often reach close to the upper level of thermal tolerance of salmon i.e. 18oC. This environment may allow for an overgrowth of opportunistic pathogens in the gastrointestinal tract of the fish, often leading to a dominance of a single or a few, and often pathogenic bacterial species. It has been postulated that this overgrowth has led to poor growth and reduced feed utilisation in salmon during these high temperature periods. There are limited studies focusing on the dynamics of the fish gut microflora and most are conducted within the thermal norm of the study species. In this study we investigated the bacterial proliferation in the gut of Atlantic salmon fed different diets through a typical temperature annual regime. A total of 279 Vibrio and 243 Pseudomonas were isolated from hind gut of Tasmanian Atlantic salmon over one year period. These strains were identified using either genus–specific primers or sequenced using 16S rRNA gene universal primers to the species level and typed using a combination of PhPlate and random amplified polymorphic DNA (RAPD)-PCR. The results indicated that Vibrio isolates mainly belonged to the species V. ichthyoenteri and V. scophthalmi species and are dominant during the warmer months of the year (i.e. November to March). These strains however, belonged to 30 clonal groups indicating their high diversity. Pseudomonas strains belonged mainly to P. fragi species and were only found during the colder months of the year. These strains also belonged to different clonal groups (33 common and 78 single types). However, persistent clones appeared in the later stages of fish growth suggesting that more stable communities of Pseudomonas strains appear during the adult stage of the salmon.