With continuous decline of Philippine forest cover, sustainable forest management and restoration are essential to restore destroyed forest ecosystems. Unfortunately, of ten most planted trees in reforestation projects in the Philippines, eight are exotic species, with large leaf mahogany (Swietenia macrophylla) being the most dominant. In this study, effect of Swietenia macrophylla in reforestation projects on native tree species was evaluated. Effects of S. macrophylla leaf litter, frequency, and canopy closure on the growth of the Philippine native species Pterocarpus indicus were investigated. Results showed that S. macrophylla leaf litter significantly inhibited the growth of P. indicus seedlings based on root collar-to-shoot height. The standardized growth rate of seedlings in plots without S. macrophylla leaf litter was significantly higher than the growth rate of seedlings in plots with leaf litter. Furthermore, there was no significant difference in the standardized growth rate of seedlings between plots without leaf litter and a control plot. On the contrary, S. macrophylla tree frequency and canopy closure showed no significant effect. These results attest to the negative effect of widely planted S. macrophylla to a valuable Philippine native tree P. indicus. With accumulating scientific evidence about negative effects of S. macrophylla on native trees, discontinued use in tree planting and reforestation efforts with active management of restoration sites previously planted with large leaf mahogany are needed.