LiDAR makes it possible to describe the 3D structure of the forest, from which species habitats can be accurately estimated, over large areas at fine resolution. However, standard airborne laser scanning (ALS) fails to describe the lower canopy in sufficient detail due to occlusion by the upper canopy. The understory is important to characterise as it harbours the majority of the forest community and is the place where regeneration takes place. Here we explored the potential of low altitude high power ALS with enhanced penetration, and denser UAV LiDAR (Unmanned Aerial Vehicle) to describe the structure of the understory. We used the recorded laser pulse extinction to build a 3D model of light transmission through the canopy. We evaluated the capacity of the light transmission model to estimate the spatial and angular variation of light in the tropical understory, considering different leaf inclination distribution functions (LIDF), compared with measurements from two different field sensors. We found that (i) LiDAR can be used to estimate the light environment in the understory in a spatially and angularly consistent way; (ii) high pulse density does not guarantee an accurate characterization of the forest structure, and penetration rate is an important characteristic to accurately describe the forest structure, especially the understory; (iii) taking into account the anisotropic nature of light transmittance improved the estimation of absolute light levels by radiative transfer.