Abstract: To explore the geographical distribution and genetic variability of Candidatus Liberibacter asiaticus（CLas）harboring diverse prophage types in China，300 CLas DNA samples extracted from leaf petioles of CLas infected citrus were collected from six provinces：Guangdong，Guangxi，Hainan，Yunnan，Sichuan and Guizhou. And surveyed for Type 1，Type 2 and Type 3 prophages by specific PCR，then sequenced，and subjected to genetic diversity analysis employing relevant bioinformatics software. The results showed that the presence of eight distinct prophage combinations among the six geographically diverse populations. Notably，the prevalence of CLas strains carrying a single prophage type was dominant，accounting for 53.3% of the samples，with Type 2 prophage being the most prevalent. Analysis of the three prophage gene loci demonstrated a higher content of A + T relative to G + C，indicating an AT preference. Recombination analysis indicated an absence of recombination signals，suggesting the absence of recombination events. The Nm value of gene flow is exceeded 1，indicating frequent gene exchange among different CLas groups. The results of the neutral test，characterized by Tajima’s D，Fu and Li’s D，Fu and Li’s F values，all being less than 0，indicated a historical expansion within the CLas population.

Key words: citrus, Huanglongbing, Candidatus Liberibacter asiaticus, prophage, genetic diversity