Huanglongbing disease (HLB), caused by Candidatus Liberobacter asiaticus, constitutes a most serious problem for the Chinese citrus industry. In this work, the use of vitrification-cryopreservation for eliminating Ca. L. asiaticus from naturally infected plants of several citrus species was investigated. Proliferating meristems were produced in vitro and excised tissue clumps were cryopreserved through vitrification using a plant vitrification solution 2. The health status of regenerated in vitro plants was checked by nested PCR. The putative HLB bacterial-free materials were subsequently re-tested after greenhouse acclimatization. Up to 98.1% of the plants obtained by cryopreservation were free from HLB bacterium, as compared with a sanitation rate of 25.3% yielded by conventional meristem tip culture. Light and electron microscopy observations of the meristem tips showed that the majority of the meristematic cells were injured either during the freezing/thawing step or during the osmotic dehydration step with plant vitrification solution 2. Only small areas of the meristematic dome survived the cryopreservation process, thereby increasing the probability of regenerating cells free of Ca. L. asiaticus. Large cells with big vacuoles and high water content, which are more likely to be infected by Ca. L. asiaticus, apparently cannot survive freezing in liquid nitrogen (LN). By contrast, small cells with dense cytoplasm located in the top layers of the meristem are more likely to escape invasion by Ca. L. asiaticus and can survive freezing in LN.