The complex and dynamic nature of aquatic ecosystems, particularly in marine environments, makes managing wound infections a significant challenge for individuals engaged in underwater activities and for aquatic organisms. Although antibiotics have played a critical role in safeguarding humans and aquatic health, their risk of drug resistance and environmental impact present substantial obstacles to long-term sustainability. Using fin rot disease in turbot (Scophthalmus maximus) caused by infection of Vibrio anguillarum (V. anguillarum) as a model, a new strategy is presented that employs a carbon dot (CD)-based antisense oligonucleotide (ASO) delivery system, combined with an adhesive hydrogel, to achieve targeted gene silencing of V. anguillarum for underwater healing. The CDs that cause enhanced cytoplasmic membrane permeability, efficiently deliver ASOs into V. anguillarum without requiring additional equipment or chemical facilitators. The specific design of the ASO sequence enables targeted silencing of empA, achieving efficiency as high as 71.2%. An adhesive hydrogel is applied to boost the local concentration of ASO/CDs at wound sites in seawater, effectively sealing the infected area and preventing fin rot disease in turbot. This study pioneer targeted bacterial gene regulation using CD-based delivery integrated with a hydrogel bandage, offering practical solutions for managing underwater bacterial diseases.