In this paper,1021 marine bacteria,which were isolated from deep sea,were screened against Sclerotinia sclerotiorum.144 Strains showed obvious antifungal activity.A resource library was established to screen a new specificity antagonistic compounds.Meanwhile,302 strains of Pseudomonas sp.were emphatically analyzed,then nineteen antagonistic Pseudomonas sp.strains with strong antagonistic activity were applied for detection of the active substance at the molecular level.The results showed that,Pseudomonas sp.1A06832 and Pseudomonas sp.SH-46 had 2,4-DAPG synthesized gene;Pseudomonas sp.1A04311,Pseudomonas sp.1A05429 and Pseudomonas sp.1A01321 had phenizine synthesized gene;Pseudomonas sp.1A06832,Pseudomonas sp.1A00318 and Pseudomonas sp.SH-46 had pyoluteorin synthesized gene;but pyrrolnitrin synthesized gene was not obtained.