The rapid uplift of Tibetan Plateau and climatic oscillations of the Quaternary dramatically shaped contemporary genetic patterns of alpine plants in Tibetan Plateau. The genetic diversity and divergence landscape patterns and the identified geographical isolation of four species containing Pedicularis longiflora, Rhodiola alsia, Sibiraea angustata and Hippophae tibetana were attained using the spatial interpolation method and Monmonier’s algorithm based on cpDNA variation. The results showed that the high genetic diversity and divergence areas were mainly highlighted within East HimalayasHengduan Mountains (HHM) region. The geographical isolation of each species was also found within the HHM region. Partial Mantel test showed that the geographical isolation had significant influence on gene flow between populations of the four species. These results verified that long-term geographical isolation resulted in high genetic divergence and diversity patterns in HHM region.