Figs and their pollinating fig wasps constitute a classic example of co-evolution. Recent molecular studies revealed that multiple cryptic fig wasp species may interact with single or different fig hosts; these species include pollinators associated with Ficus pumila. However, previous studies focused on different geographical ranges and fig varieties. The full evolutionary picture of F. pumila and its pollinating wasp, Wiebesia pumilae, has not been unraveled. Here, we collected mitochondrial COI sequences from the literature and studied the evolutionary history and phylogeography of the pollinating fig wasps of F. pumila L. var. pumila (creeping fig) and F. pumila var. awkeotsang (Makino) Corner (jelly fig). The W. pumilae contains three distinct lineages, of which Sp. 3 is mostly associated with F. pumila var. awkeotsang and Sp. 1 and Sp. 2 exclusively with F. pumila var. pumila. Wiebesia sp. 3 showed no genetic differentiation between sample collected from China and Taiwan. Besides, Sp. 3 samples from China exhibits only approximately 50% of genetic diversity compared to samples from Taiwan, suggesting Sp. 3 in China was recently introduced from Taiwan. Our study clarified the co-evolutionary relationships among F. pumila varieties and their pollinators, while showing how human activities have influenced their distribution. We also provide support for the endemism of both F. pumila var. awkeotsang and Sp. 3 in Taiwan.