Mangrove forests provide numerous valuable ecosystem services and can sequester a large volume of carbon that can help mitigate climate change impacts. Modeling mangrove carbon with robust and valid approaches is crucial to better understanding existing conditions. The study aims to estimate mangrove Above-Ground Carbon (AGC) at Loh Buaya located in the Komodo National Park (Indonesia) using novel Extreme Gradient Boosting (XGB) and Genetic Algorithm (GA) analyses integrating multiple sources of remote sensing (optical, Synthetic Aperture Radar (SAR), and Digital Elevation Model (DEM)) data. Several steps were conducted to assess the model’s accuracy, starting with a field survey of 50 sampling plots, processing the images, selecting the variables, and examining the appropriate machine learning (ML) models. The effectiveness of the proposed XGB-GA was assessed via comparison with other well-known ML techniques, i.e., the Random Forest (RF) and the Support Vector Machine (SVM) models. Our results show that the hybrid XGB-GA model yielded the best results (R2 = 0.857 in the training and R2 = 0.758 in the testing phase). The proposed hybrid model optimized by the GA consisted of six spectral bands and five vegetation indices generated from Sentinel 2B together with a national DEM that had an RMSE = 15.40 Mg C ha−1 and outperformed other ML models for quantifying mangrove AGC. The XGB-GA model estimated mangrove AGC ranging from 2.52 to 123.89 Mg C ha−1 (with an average of 57.16 Mg C ha−1). Our findings contribute an innovative method, which is fast and reliable using open-source data and software. Multisource remotely sensed data combined with advanced machine learning techniques can potentially be used to estimate AGC in tropical mangrove ecosystems worldwide.