In order to reveal the main composition of endophytic bacterial communities in nectarine and Kuqa apricot, and screen and verify the potential pathogenic bacteria, then provide the foundation for the research of storage, freshness, and prevention of soft rot disease, the endophytic bacterial communities in postharvest nectarine and Kuqa apricot in Xinjiang were analyzed by high-throughput sequencing. The pathogenic bacteria were screened by traditional isolation and culture methods, then identified based on 16S rDNA sequences analysis. The pathogenicity of strains was tested and identified by in vitro inoculation method and re-isolation method. The results showed that endophytic bacterial communities in nectarine and Kuqa apricot contained 128 operational taxonomic units (OTUs), involving 117 genera of 9 phylums. Proteobacteria was absolute dominant phyla followed by Firmicutes and Bacteroides. At the genus level, Pantoea, Bacillus, Pseudomonas and Bacteroides were the dominant microflora in nectarine, while Gluconobacter, Pantoea, Christensenella and Prevotella were the dominant population in Kuqa apricot. A potential pathogenic bacteria named XAAS-P1 related to soft rot disease was obtained, which was classified in Pantoea by phylogenetic tree construction of 16S rDNA sequence. It exerted the ability to cause the postharvest decay of nectarine and Kuqa apricot, which had consistent symptoms with natural soft rot. After 4 days inoculation, the incidence of decay was 100%, and the decay appeared 1 days earlier compared with the negative control group. Results of re-isolation and identification showed that strain XAAS-P1 was the absolutely dominant bacteria in lesion, which proved that strain XAAS-P1 was the pathogenic bacteria caused the postharvest decay of nectarine and Kuqa apricot. The study indicated that diversity of endophytic bacteria in nectarine and Kuqa apricot was rich, and the endophytic bacterium, Pantoea sp. XAAS-P1 could lead to the postharvest decay of nectarine and Kuqa apricot.