Summary Genetic analysis of individual origins works best with populations that are genetically distinct but which exchange a high rate of immigrants, conditions that don’t normally coexist since immigration acts to prevent the accumulation of genetic differences. We provide empirical results from a newly constructed habitat linkage to illustrate the unique suitability of such analysis to monitoring the re-establishment of connections between previously isolated populations. Donaghy’s Corridor links a previously isolated 498 ha fragment of rainforest to an adjacent 80 000 ha of intact forest. Starting in the final year of the planting programme that established the corridor, we trapped two species of native small mammals, the Bush Rat (Rattus fuscipes) and the Cape York Rat (Rattus leucopus), within and nearby the linkage. We used genetic data from ear clippings to determine which side of the corridor individual animals originated from, and by comparing this information to trap locations, we identified 16 long-distance movements through the corridor. As genetic analysis of origins allowed movements to be detected from a single capture event and as it reflected movement since birth, this approach yielded considerably more data than capture records alone. The combination of movement and capture records allowed species-specific assessment of corridor function, revealing that the use and occupation of the corridor was higher for Bush Rat than for Cape York Rat and was neither symmetrical nor uniform. Long-distance movements through the corridor were most common immediately after habitat restoration, dropping off as the reconstructed habitat was colonized.