Traditional methods used to monitor the aboveground biomass (AGB) and belowground biomass (BGB) of slash pine (Pinus elliottii) rely on on-ground measurements, which are time- and cost-consuming and suited only for small spatial scales. In this paper, we successfully applied unmanned aerial vehicle (UAV) integrated with structure from motion (UAV-SfM) data to estimate the tree height, crown area (CA), AGB, and BGB of slash pine for in slash pine breeding plantations sites. The CA of each tree was segmented by using marker-controlled watershed segmentation with a treetop and a set of minimum three meters heights. Moreover, the genetic variation of these traits has been analyzed and employed to estimate heritability (h 2). The results showed a promising correlation between UAV and ground truth data with a range of R 2 from 0.58 to 0.85 at 70 m flying heights and a moderate estimate of h 2 for all traits ranges from 0.13 to 0.47, where site influenced the h 2 value of slash pine trees, where h 2 in site 1 ranged from 0.13~0.25 lower than that in site 2 (range: 0.38~0.47). Similar genetic gains were obtained with both UAV and ground truth data; thus, breeding selection is still possible. The method described in this paper provides faster, more high-throughput, and more cost-effective UAV-SfM surveys to monitor a larger area of breeding plantations than traditional ground surveys while maintaining data accuracy.