Abstract: To identify the pathogen of walnut black spots in south Shaanxi regions (Shanyang County, Danfeng County, Shangzhou Prefecture) and to sort out effective bacteriostatic agents as a potential control measurement, samples of diseased walnut fruits and branches were collected for pathogen isolation and identification, as well as indoor antibacterial tests. After intensive isolation of causing from fruits, twigs and leaves, the putative causing was selected for morphological observation under scanning electronic microscope (SEM), as well as for culture traits on LB medium, physiological and chemical tests, combination of 16S ribosomal DNA and gene gyrB phylogenetic analysis. Indoor tests were implemented with a serial of concentration gradient of chitosan salts for antibacterial tests, and the effective antagonistic concentration of chitosan was evaluated by spectrophotometer at wave length 600. Results showed that isolate HB from south Shaanxi was believed the putative pathogen, and was finally assigned as a novel pathogenic variety of Pantoea vagans, which can infect leaves, twigs and fruits via slight wound and cause typical symptom of black spot in a short latent time and with a strong pathogenesis. Indoor tests showed P. vagans was sensitive to tested chitosan salts, which were believed a potential biological control agent for the black spot disease in practice, and the lowest effective concentration was assessed at 3.5 g/L for chitosan hydrochloride, at 0.5 g/L for chitosan lactate, respectively.