The present study aimed to evaluate the effects of poly-beta-hydroxybutyrate (PHB)-supplemented diets for rainbow trout (Oncorhynchus mykiss) fingerlings. For this purpose, three experimental diets were prepared to contain 0, 2, and 5% PHB; and each diet was tested in a completely randomized design for 60 days in quadruple groups of 22 fish per tank. The results showed that the inclusion of PHB in the diets did not affect the growth parameters such as mean weight gain, specific growth rate, and feed conversion ratio among treatments. There was also no effect of the PHB on chemical composition, PCR-DGGE profile of the intestinal bacterial communities, total bacterial count, lactic acid bacteria, psychrophilic bacteria as well as the intestine and the liver histopathology of fish. However, the supplementation of 2 and 5% PHB in the diet significantly reduced total coliform counts, while 5% PHB diet additionally decreased Enterobacteriaceae counts. Both inclusion ratios resulted in significantly higher intestinal villus length and width at the end of the experiment. Considering the positive effects of dietary PHB on intestinal bacterial flora and villus sizes of rainbow trout fingerlings, it can be used as an alternative microbial control agent.