Lushan Cloud Mist Tea is celebrated as one of China’s top ten famous teas, distinguished by its unique climate and geographical environment. Our analysis revealed varying levels of genetic differentiation among populations, with the most significant divergence observed between the mid-altitude JDX and low-altitude TYC groups. The low-altitude FSZ group exhibited high nucleotide diversity, suggesting a rich reservoir of genetic resources. In contrast, the low-altitude TYC group displayed comparatively low diversity, making it more susceptible to genetic drift. Additionally, the effective population size of the nine studied populations showed a degree of consistency yet indicated a increasing trend in modern times. For SIFT analysis, sift score showed the most amino acid was under TOLERATED group, indicated that the genome for this tea species was relatively stable. Overall, our findings provide essential insights into the genetic diversity and structure of Lushan Cloud Mist Tea, informing evidence-based strategies for germplasm conservation and utilization.