An influence of the intestinal microbiota in connection to first-feeding of rainbow trout (Oncorhynchus mykiss) fry was demonstrated using Illumina HiSeq sequencing. The period from the end of yolk-sac feeding to seven weeks post first-feeding was examined after administration of either a marine- or plant based diet with or without the probiont Pediococcus acidilactici. Before first feeding the main part of the sequence reads grouped to the genus Sediminibacterium probably originating from the surrounding water. The microbial abundance and diversity increased after first-feeding and the microbiota then changed towards phylum Firmicutes dominance for plant based fed fish and towards dominance of phylum Proteobacteria for the marine fed fish. After first-feeding, there were significantly higher abundances of Streptococcus, Leuconostoc and Weissella in fish fed the plant-based diet. The microbiota clustered separately according to the diet type, but only minor effects were seen from the probiont when using PCA-analysis. The constitutive transcription level of most examined immune genes increased during the ontogenic shift, but the results could not explain the differences in the composition of the microbiota dependent on diet treatment after first-feeding. The results suggest that the intestine of rainbow trout is colonised at an early state, but is guided in new and different directions dependent on the diet type.