The invention relates to a new strain of pseudoalteromonas flavipulchra and use thereof. The new strain is the JG1 strain of the pseudoalteromonas flavipulchra, and the collection number of the JG1 strain of pseudoalteromonas flavipulchra is CGMCC No.5009; and the JG1 strain produces Pfa protein during metabolism. The JG1 strain of pseudoalteromonas flavipulchr, which is disclosed by the invention, can achieve antibacterial effects by means of bacteriocin protein, small molecular compounds and the like and can inhibit various common pathogenic bacteria in aquaculture animals; and the results of animal tests on zebra fish, mantis shrimps, scallops, clams and the like indicate that JG1 has neither toxic nor side effects on animals and that the bacterial preparation prepared by using the JG1can be effectively used in actual production as a synergist in aquiculture. The Pfa protein produced in the metabolism of the JG1 strain has an obvious antibacterial effect and can be used as a preparation for improving the immunity in aquaculture animals.