ABSTRACT: During a disease outbreak, affected fish exhibit particular clinical signs, and the task in veterinary diagnostics is to identify the causative agent(s) as a prerequisite for appropriate treatment measures. In this study, we present an outbreak of a multifactorial gill disease in a cohort of ornamental koi Cyprinus carpio with gill necrosis as the main exterior clinical sign. By means of pathogen identification and determining pathogen abundance in various tissues, mortality of individual fish was found to be caused by different agents. Three out of 5 diseased individuals suffered from koi herpesvirus disease (KHVD) associated with a systemic infection with cyprinid herpesvirus 3 (CyHV-3), 1 fish succumbed to koi sleepy disease (KSD) caused by a high carp edema virus (CEV) load in the gills co-infected with CyHV-3 and flavobacteria, and the last fish had low loads of both viruses but high flavobacteria and Ichthyobodo burdens and most likely died from an interaction of these bacterial and parasitic agents. The results indicated that correct identification of the agent responsible for the observed clinical signs or mortality during co-infection might require quantitative determination of the abundance of the pathogens as well as detailed knowledge of the infection biology of these pathogens.