Citrus huanglongbing (HLB), thought to be caused by Candidatus Liberibacter asiaticus, Ca L. africanus and Ca. L. americanus, is one of the most destructive diseases of citrus worldwide. The disease has been reported in recent years in various areas of southern Iran. In a primary study in 2013, the genetic diversity of 13 representative Iranian isolates of Ca. L. asiaticus collected from provinces of Sistan and Baluchestan (Sarbaz, Ghasre-ghand), Hormozgan (Roudan, Sirmand) and Kerman (Joroft) was carried out by sequencing 16S rRNA gene, 16S/23S rRNA intergenic spacer region, the rplKAJL-rpoBC operon and outer membrane protein (omp) gene as well as simple sequence repeat (SSR) markers. Sequence analysis of the 16S rRNA gene, and the 16S/23S rRNA intergenic spacer region failed to reveal any differences between various Iranian isolates of Ca. L. asiaticus. Partial sequence analysis of the rplKAJL-rpoBC operon and omp gene showed that identity level among Iranian isolates of Ca. L. asiaticus was 99.8% to 100% and 99.2% to 100%, respectively. Phylogenetic trees based on sequences of 16S rRNA gene, 16S/23S rRNA intergenic spacer region, rplKAJL-rpoBC operon and omp gene showed that the Iranian isolates of Ca. L. asiaticus with other Ca. L. asiaticus isolates of different origins were in one group, and distinct from Ca. L. africanus and Ca. L. americanus. A number of nine SSR markers were used to study the genetic diversity of nineteen Ca. L. asiaticus isolates from Iran, Taiwan, Japan and Brazil. All nine primer pairs showed polymorphism among the isolates. A total of 38 alleles were detected using nine SSR markers. The number of alleles per locus ranged from 2 to 7, with an average of 4.22 alleles per locus. The average of the haploid genetic diversity (H) was 0.5819 for all SSR markers. Cluster analysis of the Ca. L. asiaticus isolates using the UPGMA method based on Jaccard coefficient clearly separated the isolates into four clusters including Iranian, Japanese, Taiwanese and Brazilian isolates. Iranian isolates of Ca. L. asiaticus were clustered in two major subgroups. UPGMA dendrogram separated the isolates according to their geographical origins. In conclusion, SSR markers showed the genetic diversity between and within the Ca. L. asiaticus populations. Using nine SSR markers among 19 studied isolates 18 haplotypes were identified.