This research aimed to test the effects of lactobacilli, applied to cultured pike-perch, either through hydrolyzed OTOHIME fish diet, or through Artemia nauplii, on fish growth, microbiota balance and skeletal development. On the 12th Day Post Hatching (DPH) fish were divided into following treatment groups: two groups received the combination of OTOHIME and nauplii enriched either with Lactobacillus paracasei BGHN14+Lactobacillus rhamnosus BGT10 or with Lactobacillus reuteri BGGO6-55+Lactobacillus salivarius BGHO1, and one group received OTOHIME hydrolyzed by BGHN14+BGT10 and non-enriched nauplii. Control group received non-enriched nauplii and non-hydrolyzed OTOHIME. The treatment lasted 14days and fish were sacrificed on the 26th DPH for the assessment of digestive enzyme activity and microbiota composition. Individual total lengths and individual body weights were recorded at the end of the treatments, on the 26th DPH, and also on the 45th DPH, in parallel with the evaluation of skeletal deformities and fish survival. Our results indicated positive effect of Artemia enriched with BGGO6-55+BGHO1 on fish growth, skeletal development and trypsin to chymotrypsin activity ratio (T/C), as an indicator of protein digestibility. Hydrolysis of OTOHIME was also associated with better skeletal development, higher T/C values and lower levels of Aeromonas and Mycobacterium spp., which are important fish pathogens. Though additional testing in larger cohort studies is needed, these observations are promising in terms of usage of probiotics for improved environmentally friendly production of pike-perch in Recirculating Aquaculture System (RAS).