Huanglongbing (HLB), also known as citrus greening, is the most serious disease affecting citrus production in Asia, Africa, the Americas, and the Arabian Peninsula. HLB is associated with the α-Proteobacteria “CandidatusLiberibacter asiaticus” (CLas), “Ca. L. africanus” (CLaf), and “Ca. L. americanus” (CLam). The Bangladesh citrus industry comprises mandarins, sweet oranges, pummelos, limes, and lemons. In 2017-2018, a survey was conducted for two consecutive years in 18 sweet orange growing areas of Bangladesh, and the presence of CLas in these areas was confirmed by polymerase chain reaction. HLB incidence and severity were assessed based on leaf symptoms. The results unveiled a widespread prevalence of HLB with incidence ranging between 0.08 and 56% and severity between 1.80 and 28.33. Information on the genetic diversity of CLas Bangladeshi isolates was obtained based on the presence or absence of Type 1 (SC1, NC_019549.1) and Type 2 (SC2, NC_019550.1) prophages. In silico phylogenetic analyses based on Type 1 and Type 2 prophage sequences showed the presence of four and three clusters of CLas isolates, respectively. Combined phylogenetic analyses of Type 1 and Type 2 prophages indicated the existence of four clusters of CLas isolates. Bangladeshi CLas isolates were found to harbor multiple copies of prophages. The diversity analysis revealed different CLas isolates distributed to different citrus growing areas, indicating spread through propagated materials.