Alpine forest population dynamics are sensitive to climate change. Response patterns are complex, and it is still unclear as to whether or not population dynamics are species-dependent. In this study, population dynamic patterns for alpine timberline Qilian juniper and Qinghai spruce tree species in the mid Qilian Mountains were determined from approximately 1500 C.E. by applying dendrochronological methods. The results showed that these tree species have different forest population dynamics. The Qinghai spruce recruitment rate was clearly higher than that of Qilian juniper. Furthermore, the temporal population dynamic patterns of Qinghai spruce samples taken at different sites were consistent whereas those of the Qilian juniper samples were not. Qinghai spruce population dynamics were primarily affected by temperature, with positive correlations between temperature and recruitment. By contrast, with the exception of a positive to negative shift in the relationship between temperature and Qilian juniper population dynamics, Qilian juniper recruitment significantly decreased when its density reached a relatively high level. Moreover, a shift in the temperature-recruitment relationship and a decrease in recruitment occurred simultaneously, indicating that Qilian juniper population dynamics were affected by both temperature and density. Species to species differences were also observed when compared with previous studies within the mid Qilian Mountains, confirming the existence of species-dependent population dynamic patterns. Forest recruitment dynamic patterns and tree recruitment-climate relationships may help to provide clues for future studies on forest management, conservation and utilization.