The present experimental investigation was executed to evaluate the combined effect of probiotic bacterium Bacillus coagulans along with herb Mentha piperita on histological architecture; and extent of DNA damage after challenge trial with pathogenic bacterium Aeromonas hydrophila in Catla catla. In this experiment, six dietary treatments in triplicate were formulated; C0, M3 and M6 in which M. piperita was supplemented at 0, 3, 6 g kg−1 of feed, while in dietary treatments CP, MP3 and MP6; supplementation of probiotic bacterium B. coagulans at the rate of 3000 CFU g−1 was done along with different inclusion level of M. piperita (0, 3, 6 g kg−1 of feed). Fishes were fed for 60 days on different dietary treatments. Growth performance, histological study and extent of DNA damage using comet assay was examined. Significantly (p < 0.05) high growth % gain in BW was observed in treatment MP6 followed by treatment M6. The histological analysis clearly revealed that dietary M. piperita without or with probiotic bacterium can protect the histoarchitecture of intestinal layers and liver even after challenge with A. hydrophila. Analysis of various comet parameters (tail length, olive moment, tail DNA, head DNA) affirmed that M. piperita supplemented diet can reduce the extent of DNA damage in fishes after challenge trial with A. hydrophila, however dietary supplementation of probiotic bacterium along with M. piperita can reduce the DNA damage up to larger extent confirming its combined protective effect of supplemented diets.