Abstract: The associations between plants and microbes play a critical role in plants’ resistance to pathogens. The research of correlation between microbial communities of citrus and Candidatus Liberibacter spp. might lay a foundation of biocontrol of Huanglongbing. The objective of this work was to analyze the correlation of fruit microbial communities and Candidatus Liberibacter. The bacteria and fungi of Huanglongbing symptomatic and asymptomatic citrus fruits were characterized with Illumina amplicon sequencing. The relative abundance of Candidatus Liberibacter in the fruits positively was correlated with HLB symptom and alpha diversity. The community structure of bacteria and fungi in symptomatic was significantly differ from asymptomatic analyzed by beta-diversity. Network analysis of microbial community shown that Enterococcus, Fusarium and Sporobolomyces co-occurred with Candidatus Liberibacter. Shigella and Agrobacterium displayed a negative interaction with the pathogen. This work firstly reported huanglongbing alter the microbial community of citrus fruits, and confirmed several microbes significantly interacted with huanglongbing pathogen Candidatus Liberibacter.