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The basis for the δ¹³C values of plant tissues used to infer past ecological environments is their relationships with modern ecological conditions. A total of 71 pairs of pollen and leaf samples were collected from <i>Pinus yunnanensis</i>, an endemic species of the Yunnan plateau, in northwestern Yunnan, China. Their carbon isotopic composition was examined to investigate the two tissues’ difference of stable carbon isotopes, possible factors affecting their δ¹³C values, and their distinctiveness within <i>Pinus</i> and Pinaceae. Our study showed that pollen δ¹³C values range from −32.92 to −26.34‰ with an average of −30.88‰, whereas leaf δ¹³C values vary between −33.79 and −28.96‰ with an average value of −31.2‰, suggesting an isotope fractionation between the two tissues. A statistically significant negative correlation between the pollen δ¹³C values and altitudes of the sampling sites as well as no significant correlation between the leaf δ¹³C values and altitudes suggested that pollen may be more sensitive to some climatic parameters than leaf. A comparison of the pollen and leaf δ¹³C values from <i>Pinus yunnanensis</i> with the available data from other <i>Pinus</i> species and other genus species of Pinaceae indicated that the pollen and leaf δ¹³C values of <i>Pinus yunnanensis</i> are the lowest, partially due to the effects of water availability.