The usage of probiotics proved advantageous in aquaculture due to its positive impact on fish growth, immune response and environment. This study was aimed to assess the effects of probiotics on growth, survival and histometry of intestine and liver in Gangetic mystus (Mystus cavasius) using two separate experiments for a period of 8 weeks (in aquaria) and 16 weeks (in earthen ponds). Three different probiotic treatments were incorporated i.e. commercial probiotic one; CP-1 (T1), commercial probiotic two; CP-2 (T2), Lab developed (Lab dev.) probiotic (T3) including a control. The results indicated that the probiotics usage especially Lab dev. probiotic (T3) significantly improved the growth parameters such as weight gain (g) and specific growth rate (SGR, %/day) as well as ensured better feed conversion efficiency. Zero mortality was observed in aquaria whereas probiotic application enhanced survivability in earthen ponds. Moreover, all probiotic treatment exhibited positive results for different histo-morphometric features of intestine and liver. Mucus secreting goblet cells and fattening of mucosal fold increased significantly with probiotic usage. The amount of regular shaped nucleus was maximum in T3 with least intra cellular distance between liver tissues in earthen ponds. The greatest value for hemoglobin with lowest glucose level was observed in T3 as well. Furthermore, probiotic ensured low concentration of ammonia during culture. Overall, it was anticipated that the application of probiotics in Gangetic mystus culture resulted positive effect on its growth, feed utilization, survivability, histo-morphometry, immunity and hematological parameters.