The skin is a barrier between the body and the environment that protects the integrity of the body and houses a vast microbiota. By interacting with the host immune system, the microbiota improves wound healing in mammals. However, in fish, the evidence of the role of microbiota and the type of species on wound healing is scarce. We aimed to examine the wound healing rate in various fish species and evaluate the effect of antibiotics on the wound healing process. The wound healing rate was much faster in two of the seven fish species selected based on habitat and skin types. We also demonstrated that the composition of the microbiome plays a role in the wound healing rate. After antibiotic treatment, the wound healing rate improved in one species. Through 16S rRNA sequencing, we identified microbiome correlates of varying responses on wound healing after antibiotic treatment. These findings indicate that not only the species difference but also the microbiota play a significant role in wound healing in fish.