The present study examined a co-infection caused by Yersinia ruckeri and Pseudomonas fluorescens in three different rainbow trout farms in Muğla, in the Southwest Aegean Region of Turkey, leading to heavy losses with up to 40% mortality. The diseased fish had melanosis, haemorrhagic skin lesions, deep ulcers on the caudal fin base and tail rot. Necropsy detected enlarged liver and spleen, haemorrhage in peritoneal and subperitoneal membranes, pyloric caeca, perivisceral fat and lower intestines. Biochemical and molecular identification was performed, and histopathology and antibiotic susceptibility tests were conducted on the infected tissues. API 20E biochemical identification tests and PCR amplification proved that the causative pathogens were Yersinia ruckeri and Pseudomonas fluorescens. In histopathological studies, degeneration and desquamation in the epidermis were observed. Both isolates were resistant to clindamycin, ampicillin, oxolinic acid and penicillin. The clinical and pathological signs of both pathogens were observed in the infection experiment. The mortality rates of the experiment groups were calculated 60%, 40% and 80% in Group A (infected with 9.4 × 108 CFU/ml Y. ruckeri), Group B (infected with 1 × 108 CFU/ml P. fluorescens) and Group C (injection of both pathogens), respectively, while the control group had no mortality or clinical signs of the disease. The co-infection caused by Y. ruckeri and P. fluorescens seems to be an important threat that may spread across the region. To date, no natural co-infection by these two Gram-negative bacteria has been reported from rainbow trout. These pathogens may cause sudden outbreaks together with high mortality which is difficult to control.