Intestinal microbiome of commercial aquatic species is an important fish farming factor that prevents or reduces economic losses. Heterotrophic bacteria that inhabit intestinal mucosa are involved in digestion, vitamin synthesis, immune modulation, and resistance to pathogens. Age-related changes in the composition of heterotrophic bacterial flora affect health status, nutrient absorption efficiency, and growth rate during ontogenesis. Most studies focus on the luminal microbiota, while the mucosal layer remains understudied despite its reliable impact on the immune system. The current lack of data on the agerelated bacterial dynamics limits the development of age-specific diet strategies and disease prevention. This article presents data on the correlation between the age of rainbow trout (Parasalmo mykiss (Walbaum, 1792)) and the composition of cultured heterotrophic microflora. The research featured 40 fish aged from one to two years and grown on fish farms in the Republic of Karelia, Russia. The bacteria isolated from their intestinal mucosa were identified using standard microbiological methods. The analysis involved the morphotype and biochemical activity, as well as the tinctorial and cultural characteristics of the isolates. The species identification relied on the MALDI-TOF technology. The indices of dominance (Simpson, Berger–Parker), evenness (Pielou), diversity (Shannon), and richness (Margalef, Menhinick) made it possible to reveal that the heterotrophic component of the rainbow trout intestinal bacteria was a stable microbial community with a predominance of Bacillaceae and Enterobacteriacae enterobacteria, as well as Gram-negative non-fermentative bacteria. The index values corresponded to moderate α-diversity, which is typical of natural communities that tend to combine several abundant species with some rare taxa. These results may help develop a scientific system for managing the gastrointestinal microflora of commercial fish to improve their health and productivity.