In the present study, the structure of the intestinal microbiota of Atlantic salmon (Salmo salar L.) was studied using culture and culture-independent methods. Three adult specimens of S. salar were collected from a commercial salmon farm in Chile, and their intestinal microbiota were studied by partial sequencing of the 16S rRNA gene of pure cultures as well as of clone libraries. Out of the 74 bacterial isolates, Pseudomonas was the most predominant genus among cultured microbiota. In clone libraries, 325 clones were obtained from three adult fish, and a total of 36 operational taxonomic units (OTUs) were identified. This indicated that lactic acid bacteria (Weissella, Leuconostoc, and Lactococcus genera) comprised more than 50 % of identified clones in two fishes. This was in contrast with the high dominance of a single OTU (99 sequences) of Aliivibrio sp. related to the pathogenic Aliivibrio salmonicida species and the absence of lactic acid bacteria in the third fish, suggesting a condition of an asymptomatic non-healthy carrier. It is clear that molecular identification of 16S rRNA gene libraries obtained from intestinal content samples is effective in determining the overall structure of the intestinal microbiota of farmed Atlantic salmon enabling detection of a minority of taxa not previously reported as part of the intestinal microbiota of salmonids, including the genera Hydrogenophilus, Propionibacterium, Cronobacter, Enhydrobacter, Veillonella, Prevotella, and Atopostipes, as well as to evaluate the health status of farmed fish when evaluating the dominance of potential pathogenic species and the incidence of lactic acid bacteria.