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Balancing forest conservation with resource extraction by local people is challenging. In the mountain forests of Bwindi Impenetrable National Park in Uganda, this was addressed by permitting regulated access to certain forest products in specific areas by authorized local people. However, it remained unclear whether harvest levels were biologically sustainable. Here, we used matrix population models and long-term data to examine the impacts of bark harvesting on population dynamics of two important medicinal plants, Rytigynia kigeziensis and Ocotea usambarensis, in Bwindi. Only 4% of R. kigeziensis and 3% of O. usambarensis stems (>1.3 m height) showed signs of bark harvest, mostly mild harvesting. We found that the harvested populations of both species appeared stable or will moderately grow in the long run. Modelled population growth rates were mostly determined by survival probabilities. Similarity between the stable stage distributions predicted by the model and observed population structures suggests that our estimated vital rates (growth, recruitment and survival rates) are a reasonable representation of actual values in these populations. Thus, recent harvest levels of R. kigeziensis and O. usambarensis appear sustainable. Nonetheless, monitoring of harvested and unharvested populations by tagging, marking and remeasuring individuals should continue for both species.