Huanglongbing (HLB), a destructive plant bacterial disease, severely impedes worldwide citrus production. In our previous reports, we revealed the molecular mechanisms of host plant responses that underlie thermotherapy against HLB. In this study, we investigated the molecular mechanism underlying heat or tetracycline treatments on the HLB bacterium, 'Candidatus Liberibacter asiaticus' (Las) by focusing on Las prophage/phage conversion under stress conditions. By comparing the prophage FP1 and FP2 copy number to the copy number of 16S rDNA in HLB-affected plants, we found that the relative copy number of both FP1 and FP2 increased significantly, ranging from 3.4- to 6.7-fold change when Las-infected samples underwent a temperature shift from 23 to 37, 42 or 45 °C. When treated with tetracycline at 50-150 and 200-250 µg/ml, respectively, the relative copy number of both FP1 and FP2 increased by 3.4- to 6.0-fold. In addition, analyses of Las prophage structural gene and antirepressor gene copy numbers showed similar trends for all treatments. Furthermore, transmission electron microscopy provided direct evidence of lysogenic to lytic conversion upon temperature increase. These results not only provide new insight into the molecular mechanisms underlying heat or tetracycline treatment but also suggest a novel HLB control strategy by enhancing the endogenous conversion from Las prophages to phages.