Witches' broom disease of lime (WBDL) is the most devastating disease of acid lime in Oman, UAE and Iran. The disease was reported in Oman in the 1970s, in the UAE in the 1980s and in Iran in the 1990s and it is caused by Candidatus Phytoplasma aurantifolia'. WBDL killed over one million lime trees in Oman, the UAE and Iran. Despite efforts to characterize the disease, no study attempted to characterize the relationship among 'Ca. P. aurantifolia' from the three countries. This study utilized sequences of the 16S rRNA, imp and sech genes to characterize 57 isolates collected from Oman (38), the UAE (9) and Iran (10). Phylogenetic analysis using the 16S rRNA gene separated all isolates into 4 clusters, with the first cluster consisting of 48 (84%) isolates from Oman, the UAE and Iran. Analysis indicated that all isolates shared a high level of nucleotide similarity based on sequences of the 16S rRNA (>98.9%). The level of genetic divergence was low using 16S IRNA (0-0.045) sequences and it was found to be very low based on imp (0-0.18) and secA genes (0-0.026). Isolates collected from Musandam showed the highest level of diversity, followed by isolates from Iran and Al-Ain, UAE. Analysis of presence of phytoplasma in lime seedlings from nurseries showed that 90% of the seedlings were infected by phytoplasma. This study shows the presence of low level of diversity among phytoplasma VILA isolates from Oman, UAE and Iran. It also showed that seedlings from commercial nurseries in Oman can contribute to the movement of phytoplasma between geographical regions. The study discusses factors affecting diversity of phytoplasma and the potential ways for managing the disease.