Global aquaculture has seen an unprecedented expansion in recent years partly due to “functional feeds” that is known to improve feed utilization, fish growth performance and resilience to infectious disease. Nevertheless, a knowledge gap exists about how dietary phytase might influence intestinal bacteriomes of farmed fish. We therefore performed 16S rRNA gene-based community profiling. The remarkably uniform mucosal bacteriomes of rainbow trout (median Bray-Curtis similarity index 0.76 ± 0.09) fed the control diet were dominated by lactic acid bacteria (LAB) from putative phytase producing genera Lactococcus and Leuconostoc that likely originated from plant-based feed ingredients. Mucosal bacteriomes developed into uniform communities instead dominated by Mycoplasma-bacteria (median Bray-Curtis similarity index 0.55 ± 0.13) in response to the optimal amount of dietary phytase (0.15 g/kg feed). Both community types had a similar median species richness with 933 ± 301 and 1005 ± 678 bacterial taxa, respectively. A functional genomics analysis revealed that especially genes for amino acid and carbohydrate metabolism/transport were enriched in the LAB-dominated mucosal bacteriomes supporting their role as providers of otherwise inaccessible nutrients from for example dietary fibres. In contrast, only genes for energy production and conversion were marginally enriched in Mycoplasma-dominated communities. It is plausible that a combination of nutrient and mucosal space/attachment site competition is behind the observed shift in mucosal communities. Our results confirm previous reports that dietary phytase improve significantly both fish growth performance and feed utilization (p < 0.05). Moreover, dietary phytase is recommended for use in aquaculture as the enzyme apparently can facilitate the establishment of beneficial Mycoplasma-dominated bacteriomes in the intestinal mucosa of farmed rainbow trout.