Huanglongbing (HLB) disease is threatening citrus production worldwide. The causative agent is “
Candidatus
Liberibacter asiaticus.” Prior work using mapping-based approaches identified prophage-like sequences in some “
Ca.
Liberibacter asiaticus” genomes but not all. Here, we utilized a
de novo
approach that expands the number of prophage-like elements found in “
Ca.
Liberibacter asiaticus” from 16 to 33 and identified at least one prophage-like sequence in all “
Ca.
Liberibacter asiaticus” strains. Furthermore, we identified a prophage-like sequence type that is a remnant of an integrated prophage—expanding the number of prophage types in “
Ca.
Liberibacter asiaticus” from 3 to 4. Overall, the findings will help researchers investigate the role of prophage in the ecology, evolution, and pathogenicity of “
Ca.
Liberibacter asiaticus.”