The gastrointestinal (GI) tract microbial communities of commercially farmed Atlantic salmon (Salmo salar L.) were examined using culture-based techniques and by pyro-tag sequence analysis. The aim of this study was to identify key GI tract bacteria that represent drivers for salmon health and assess how community structure develops during intensive feeding from smolt through to harvestable adult fish in south-eastern Tasmania. Faecal samples were collected from fish in two different pens fed different commercial winter or summer diets over a 13 month production period. Bacterial numbers increase with an increase in fish weight but these changes better correlate with changes in water temperature. Results show that, in smolt hind-gut communities were dominated by Gram-positive fermentative bacteria. Members of family Vibrionaceae were more dominant in growing salmon and nearly completely dominate faecal communities in mid-summer. Curiously filamentous cyanobacteria which may derive from the farm environment or fresh water during bathing were also abundant in summer months. As time progresses towards winter and harvest, a range of different bacterial genera become more prominent in a diet dependent manner but this corresponds to a decline in culturable bacterial populations. The overall data demonstrates the dynamism of hind gut communities in salmon and shows its strong relation to water temperature and diet. The study provides a baseline such that productivity issues can be better assessed within salmon mariculture system, and for diet formulation improvements that may be needed to meet future challenges to the salmon aquaculture industry.