Puffy snout syndrome (PSS) is a chronic illness in captive-held scombrid fish. Here we evaluated the host physiological response to PSS and characterized the host-associated viral community of Pacific mackerel (Scomber japonicus) using high-throughput sequencing techniques. There were three groups assessed in this study asymptomatic-captive mackerel, symptomatic-captive mackerel, and wild-caught mackerel.