Abstract: To identify pathogen species causing soft rot of tobacco seedlings in greenhouses, tobacco seedlings with typical soft rot were sampled to isolate pathogens by organization separation method. The species of pathogens were identified by physiological and biochemical characteristics and 16S rDNA sequence analysis, and the pathogenicity of isolated pathogens to four tobacco cultivars (K326, Zhongyan 100, Dabaijin 599 and Gexin 3) was detected. The results showed that the purified strain YCS-1 was a bacterial disease which could infect different tobacco cultivars. The physiological and biochemical characteristics of YCS-1 were consistent with those of Raoultella. BLAST alignment and phylogenetic tree analysis suggested that YCS-1 and R.ornithinolytica were located in the same branch, and their sequence homology reached 99%. Therefore, YCS-1 was identified as R.ornithinolytica.