Citrus Huanglongbing (HLB), the highly destructive disease which has been threatening citrus production worldwide, is caused by the yet unculturable bacteria, "Candidatus Liberibacter spp.". HLB can be spread with insect vector and contaminated seedlings. In recent years, with the rapid development of DNA sequencing technology and bioinformatics, genomic analysis had become widely used for HLB research, and had provided the new strategies to overcome the research bottleneck caused by difficulties in bacterial culture. The genomic analysis of "Candidatus Liberibacter spp." not only helps to explore the interaction between "Candidatus Liberibacter spp." and host plant, but also provides an important theoretical basis for resistance cultivation and early detection of HLB. This review summarizes the research progress in citrus HLB and describes the current sequencing strategy and genomic characterization of "Candidatus Liberibacter spp.", with an emphasis on the research progress in genomic analysis of pathogenic mechanism, genetic diversity and molecular detection of "Candidatus Liberibacter spp.".