Prevalence of antibiotic resistance among gut associated bacteria of two indigenous freshwater ornamental fishes were analyzed in this study. A total of 56 bacteria was isolated from the gut of Aplocheilus lineatus and Etroplus maculatus. Total viable count (TVC) of heterotrophic bacteria ranged between 1.7 x 10⁶ to 6.8 x 10⁶and 0.2 x 10⁴ to 0.65 x 10⁷cfu per gram in gut of Etroplus maculatus and Aplocheilus lineatus respectively. Predominant genera encountered in the gut of A. lineatus were Lactobacillus, Bacillus, Micrococcus, and Aeromonas, while that of E. maculatus was dominated by Micrococcus followed by Bacillus, Lactobacillus and Vibrios. The isolates were subjected 11 different antibiotics belonging to 7 different classes such as aminoglygocides (streptomycin, gentamicin), quinolones (nalidixic acid), fluorquinolones (ciprofloxacin), tetracyclines (tetracycline), penicillin (carbenicillin), cephalosporins (cephalothin, cefpodoxime), sulphonamides (sulfafurazole, trimethoprim). Antibiotic resistance among the gut associated bacteria from A. lineatus was relatively  lower when compared to those from the gut of E. maculatus. Multiple antibiotic resistance (MAR) indexing of the isolates revealed that nearly 50% of the bacterial isolates of E. maculatus were multiple drug resistance, while in A. lineatus it was found to be 38.41%.The MAR index of the isolates ranged from 0.09 - 0.36 in A. lineatus; 0.09 - 0.63 in E. maculatus.While most isolates from the gut of both the fishes were resistant to Cefpodoxime, none of the isolates were resistant to Gentamicin. Though the prevalence of antibiotic resistance among gut of these indigenous fishes are relatively lower when compared those from the gut of cultured ones, considerable pollution of the natural waters are providing ideal environment for the emergence of drug resistance mutants and subsequent colonisation in the gut of fish fauna of these waters.