Gut microbiota are integral to the host, and have received increased attention in recent years. However, information regarding the intestinal microbiota of many aquaculture animals is insufficient; elucidating the dynamics of the intestinal microbiota can be beneficial for nutrition, immunity, and disease control. In this study, we used 16S rRNA sequencing to observe changes in the intestinal microbiota of gibel carp (Carassius auratus gibelio) associated with cyprinid herpesvirus 2 (CyHV-2) infection. Our results indicate that the diversity of the intestinal microbiota was strongly reduced, and the composition was dramatically altered following CyHV-2 infection. The most dominant species in healthy fish were Cetobacterium, Rhodobacter, and Crenothrix; meanwhile, Cetobacterium, Plesiomonas, Bacteroides, and Flavobacterium were the most abundant species in sick fish. Plesiomonas was highly abundant in infected samples, and could be used as a microbial biomarker for CyHV-2 infection. Chemical properties of the aquaculture water were significantly correlated with the microbial community structure; however, it is difficult to determine whether these changes are a cause or consequence of infection. However, it may be possible to use probiotics or prebiotics to restore the richness of the host intestinal microbiota in infected animals to maintain host health.