Injuries are an undesirable situation in fish kept in aquariums. The use of antibiotics in wound healing is not preferred due to the development of antibiotic resistance in bacteria and for economic reasons. This study was conducted to demonstrate the efficacy of Juniperus root extract in healing experimentally induced incised wounds in yellowtail acei. Wound closure time, morphology, malondialdehyde content, glutathione s-transferase activity, changes in gene expression levels, non-dispersibility of the extract in aqueous environment, and retention on the wound were analyzed. In the antibiotic group, the scarring of the wound was observed on the sixth day. On the other hand, in the root extract group, wound healing was completed on the second day. In addition, a significant decrease in malondialdehyde and glutathione s-transferase levels was observed in the extract group compared to the control group. It was found that SWS2a, RH2B, and LWS gene expression levels started to decrease during wound healing at the end of the second day in the extract-treated group. In the antibiotic group, the same effect was observed on the seventh day. Important properties of the extract used, such as not dispersing in the water environment and remaining on the wound, were also determined. It would be useful to continue the experiments with Juniperus root extract, which has been shown to be effective in wound healing, with microscopic studies on aquaculture and diseases.