Herein, we described the most evident effects of selective logging on the structure and composition of a lowland tropical rain forest in San Isidro, Choco, Colombia. Structure and composition of woody elements from 10 plots (2 x 50 meters = 0.1 ha) located in a natural forest and 10 plots (2 x 50 meters = 0.1 ha) located in a forest used for selective logging was analyzed. We report a greater number of species, genera and families of woody plants in the natural forest than in forest with selective logging. In addition, forest where selective logging takes place experienced a significant reduction in number of canopy-dominant trees, as well as in number of species and genera of the 10 more representative families found in the analyzed natural forest. We predict that this documented reduction in the natural forest structural complexity will have a deleterious impact on the population dynamics of fauna in the study area, particularly on canopy-dependent fauna.