Citrus Huanglongbing (HLB) is a bacterial disease that affects citrus trees and is considered the most severe citrus plant disease in the world [1]. Despite their major impact on agronomy, the epidemiology, ecology, and evolution of the three Gram-negative phloem-restricted Candidatus Liberibacter species associated with the disease remain largely unknown due to their non-culturable nature. Among them, af) are the two epidemiologically active species distributed in the citrus-growing regions [2]. These phytopathogenic bacteria are known pathogenicity and adaptability to their host plants and insect vectors [3-5]. The aim of this study was to investigate the integrated prophage-like sequence of CLas by assembling and exploring its first de novo genome assembly from Réunion (V1R1). Two prophages were identified into this 1,271,573 bp single contig de novo assembly, including one prophage that belonged to a new Type 5 CLas prophage (P-V1R1-5) which is highly similar to one prophage previously identified in several CLaf genomes. PCR amplifications specifically targeting this prophage suggested that most CLas strains from Réunion and all CLaf strains from Madagascar and Réunion have incorporated at least parts of this prophage. The identification of this first interspecies variable prophage not only expanded our knowledge of CLas genomic diversity in Réunion, but also provided new insights into the potential role of horizontally transferred elements in the evolution and biology of the sympatric HLB-causing Ca. Liberibacter species.