The Burkholderia cepacia complex isolates causing bacterial fruit rot of apricot were characterized by speciesspecific PCR tests, recA-HaeIII restriction fragment length polymorphism (RFLP) assays, rep-PCR genomic fingerprinting, recA gene sequencing, and multilocus sequence typing (MLST) analysis. Results indicated that the isolates Bca 0901 and Bca 0902 gave positive amplifications with primers specific for B. vietnamiensis while the two bacterial isolates showed different recARFLP and rep-PCR profiles from those of B. vietnamiensis strains. In addition, the two bacterial isolates had a higher proteolytic activity compared with that of the non-pathogenic B. vietnamiensis strains while no cblA and esmR marker genes were detected for the two bacterial isolates and B. vietnamiensis strains. The two bacterial isolates were identified as Burkholderia seminalis based on recA gene sequence analysis and MLST analysis. Overall, this is the first characterization of B. seminalis that cause bacterial fruit rot of apricot.