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Selective logging is one of the most prominent land uses in tropical forests and although it involves harvesting a limited number of trees, the impact on forest structure, composition and aboveground biomass can be significant. Although these impacts are well documented, what is little known is the extent to which selective logging affects tree floristic composition and its recovery process. Understanding how floristic composition is affected by logging activities is essential for determining subsequent cutting cycles, for the maintenance of carbon stocks and for biodiversity conservation. This research investigates the effect of logging on long-term trends on the recovery of species composition in a tropical forest using a unique logging experiment where measurements have been taken annually over a period of 25 years. Changes in 12 long-term 1-hectare (ha) permanent plots were assessed where different selective logging intensities occurred. In the first years after logging, floristic composition differed widely between intact and selectively logged forests, with exploited areas deviating from pre-logged composition. Over time, exploited areas shifted towards the original composition, with more pronounced changes in this trend after similar to 13 years. Shifts in floristic composition were caused mainly by a significant increase in light-demanding fast-growing pioneer species and their subsequent continuous high mortality rates after 13 years of the recovery process. In contrast, the control plots showed similar shifts in composition over time, suggesting external factors such as long-term climate changes may be driving these shifts. The results suggest that 25 years after an experimental selective logging has taken place, floristic composition tends to recover closer to the pre-logged status. Thus, in the absence of further human disturbances, experimental selectively logged forests in low to moderate intensities are compatible with biodiversity conservation, at least during the first cycle of exploitation. Reconciling conservation strategies with the recovery of stocks of commercial timber species would be greatly improved by using these results and lead towards more sustainable forest management plans.