The prevalence of juvenile Pacific abalone disease without apparent external lesions in the Chinese province of Fujian has led to mass mortality in 2018. A novel method for screening abalone pathogen was developed based on the importance of mucus in innate immunity. We identified the pathogenic bacterial strain of abalone by bacterial isolation, sequence analysis, and experimental challenges in vitro and in vivo. We verified that the abalone mortality rates were high when exposed to Pseudoalteromonas shioyasakiensis strain SDCH87 at 28 °C. This opportunistic pathogen had an outstanding growth ability in mucus and disrupted the first line mucosal immunity in the pedal within three days. To our knowledge, this is the first report that P. shioyasakiensis is a severe opportunistic pathogen of abalone, which indicated pedal was the lesion, in the context of a heatwave.