Dispersal that unites spatially subdivided populations into a metapopulation with source–sink dynamics is crucial for species persistence in fragmented landscapes. Understanding such dynamics for pollinators is particularly urgent owing to the ongoing global pollination crisis. Here, we investigated the population structure and source–sink dynamics of a pollinating wasp (Wiebesia sp. 3) of Ficus pumila in the Zhoushan Archipelago of China. We found significant asymmetry in the pairwise migrant numbers for 22 of 28 cases on the historical timescale, but only 2 on the contemporary timescale. Despite a small population size, the sole island not colonized by a superior competitor wasp (Wiebesia sp. 1) consistently behaved as a net exporter of migrants, supplying large sinks. Comparable levels of genetic diversity, with few private alleles and low genetic differentiation (total FST: 0.03; pairwise FST: 0.0005–0.0791), were revealed among all the islands. There was a significant isolation-by-distance pattern caused mainly by migration between the competition-free island and other islands, otherwise the pattern was negligible. The clustering analysis failed to detect multiple gene pools for the whole region. Thus, the sinks were most likely organized into a patchy population. Moreover, the estimates of effective population sizes were comparable between the two timescales. Thus the source–sink dynamics embedded within a well-connected population network may allow Wiebesia sp. 3 to persist at a competitive disadvantage. This study provides evidence that metapopulations in the real world may be complicated and changeable over time, highlighting the necessity to study such metapopulations in detail.