Outbreaks of diseases in farmed fish remain a recurring problem, despite the development of vaccines and improved hygiene standards on aquaculture farms. One commonly observed bacterial disease is tenacibaculosis, which is attributed to members of the Bacteroidetes genus Tenacibaculum, most notably T. maritimum. The impact of tenacibaculosis on fish microbiota remains poorly understood. In this study, we analyse the microbiota of different tissue types of commercially reared Asian seabass (Lates calcarifer) that show symptoms of tenacibaculosis and compare the microbial communities to those of healthy and experimentally infected fish (exposed to diseased farm fish).