Abstract: Background and Objective: Now a days, the need for remarkable disease resistance, growth of aquatic organisms and feed competence has brought about the employ of probiotics in aquaculture field. The objective of the present study was to isolate probiotic bacterial strains from fish intestines and screen them by in vitro testing of their antagonism to pathogens and bioencapsulation efficacy. Materials and Methods: Six bacteria were isolated from marine fish gut and identified by biochemical test. All six isolates were assessed in vitro for its inhibitory activity against common fish pathogens of Aeromonas hydrophila and Vibrio harvey by well diffusion assay. Based on the antimicrobial activity, the Enterococcus, Streptococcus and Bacillus were selected for assaying probiotic properties of acid tolerance, bile salt concentration and auto aggregation assay. The 24 h old Artemia salina nauplii were selected for probiont encapsulation study. Results: The isolates Enterococcus, Streptococcus and Bacillus were confirmed as probionts by above mentioned three methods. The research of encapsulation studies exposed that the gut loading and evacuation time of Artemia nauplii differed according to the oils and probiotics used for the trials. Probiotics take less time for gut loading and retention when compared to oils. Conclusion: The findings of this study indicated that the indigenous fish gut bacteria provided benefit to the culture fishes in terms of pathogen protection and increasing growth potential and thus fulfilled the major requirements of being effective probiotics