Tree parameter determinations using airborne Light Detection and Ranging (LiDAR) have been conducted in many forest types, including coniferous, boreal, and deciduous. However, there are only a few scientific articles discussing the application of LiDAR to mangrove biophysical parameter extraction at an individual tree level. The main objective of this study was to investigate the potential of using LiDAR data to estimate the biophysical parameters of mangrove trees at an individual tree scale. The Variable Window Filtering (VWF) and Inverse Watershed Segmentation (IWS) methods were investigated by comparing their performance in individual tree detection and in deriving tree position, crown diameter, and tree height using the LiDAR-derived Canopy Height Model (CHM). The results demonstrated that each method performed well in mangrove forests with a low percentage of crown overlap conditions. The VWF method yielded a slightly higher accuracy for mangrove parameter extractions from LiDAR data compared with the IWS method. This is because the VWF method uses an adaptive circular filtering window size based on an allometric relationship. As a result of the VWF method, the position measurements of individual tree indicated a mean distance error value of 1.10 m. The In this study, the accuracy of LiDAR-derived biophysical parameters in mangrove forests using the VWF and IWS methods is lower than in coniferous, boreal, pine, and deciduous forests. An adaptive allometric equation that is specific for the level of tree density and percentage of crown overlap is a solution for improving the predictive accuracy of the VWF method.