In this study altogether 109 autochthonous gut bacteria were screened from 4 fish species (Labeo rohita, Labeo bata, Catla catla and Puntius javanicus), of which 13 isolates displayed antagonism to 4 fish potent pathogens, namely Aeromonas salmonicida, Aeromonas hydrophila, Pseudomonas fluorescens and Aeromonas sobria. Eight promising isolates were further evaluated for extracellular enzyme production, non-hemolytic activity, bile tolerance and identified by 16S rRNA sequencing. Strains CCF7 (identified as Bacillus sp.), CCH9 and PJH1 (identified as two strains of Bacillus amyloliquefaciens) exhibited high score in antagonism assay and fulfilled other probiotic criteria, including safety aspects. However, application of these probiotics in aquaculture industries requires in vivo experiments and other information like immune modulating efficiency and binding ability on gut.