Four fungi, strain 231#, 320#, 322#, and 333# were isolated from infected jujube, sweet cherry, apricot, and blueberry fruit. All the fungal pathogens were identified as Alternaria Nees by morphological characterization. Analysis of rDNA ITS sequence showed that strain 320# and 322# were both closely related to A. alternata (AY625056.1). In contrast, strain 231# and 333# showed close phylogenetic relationship with A. tenuissima (KP324980.1). The biolog microbial identification system with FF MicroPlate was applied in the 95 carbon and nitrogen sources utilization tests, and the carbon metabolic fingerprinting showed that four strains have 86 carbon sources in common, including 78 optimal carbon sources and 8 unavailable carbon sources.Moreover, strain 231# was closely related to A. alternata (Fr.) Keissl. There were some difference between rDNA ITS sequence and carbon metabolic profiling of four strains.