Experimental manipulations of root competition on naturally established seedlings were conducted across canopy openness and soil depth gradients in a selectively-logged, semideciduous forest on limestone-derived soils in southeastern Mexico. We studied the relatively shade intolerant mahogany (Swietenia macrophylla, Meliaceae) and shade tolerant ramón (Brosimum alicastrum, Moraceae). Both species are ecologically and economically important canopy trees that respond differently to selective logging, hurricanes, and fires on the Yucatan Peninsula. The canopy openness gradient used in the experiment was created by low-intensity selective logging operations. The responses of naturally occurring seedlings of both species growing within 20–30 cm deep circular trenches were examined over a 19-month experimental period. Trenching resulted in increased relative growth in diameter, stem length, and number of leaves of Swietenia compared with controls, but had no effect on Brosimum relative growth or on seedling survival of either species. There was no significant interaction between increased light availability and trenching on Swietenia seedlings, perhaps because of their larger size in gaps. Trenching effects on Swietenia were not greater during the dry season, suggesting that surface trenching affected growth during transitions between seasons. Contrasting responses of Swietenia and Brosimum seedlings to changes in soil and light environments point to the need for diversity in silvicultural practices in seasonally-dry tropical forests such as the community-managed forest examined in this study.