Citrobacter freundii is a zoonotic pathogen that causes skin injuries and high mortality rates in fish. This study aims to determine the presence of C. freundii and antibiotic susceptibility in 50 goldfish (Carassius auratus) skin wounds with local bleeding between the ages of 8–18 months in three regions (A, B, and C) located in the West of Turkey. C. freundii (22/50; 44%) strains were isolated from wound swab samples by phenotypic and genotypic methods. C. freundii isolates were positive for H2S, mannitol, and indole, and were negative for the gas formation and urea. All C. freundii isolates showed 96% similarity to C. freundii strain BAO2749 according to the Sanger sequence method. Isolates were also resistant to ampicillin at 57.09% and susceptible to cefoperazone and sulfamethoxazole-trimethoprim by 100%. Statistical analyses were evaluated at a confidence interval of 95%. A p value < 0.05 was considered statistically significant. In conclusion, C. freundii isolates can play a significant role in the pathophysiology of infections in goldfish (Carassius auratus). It can also cause commercial losses in businesses. For this reason, it will be beneficial to control C. freundii pathogenicity in aquarium fish with prophylactic applications to improve product quality and treat diseases in ornamental fish farming.