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Despite comprising only one per cent of global forests, mangroves provide vital ecological and economic benefits to their ecosystems. Due to its decreasing extent over the past decade, there is a rise in research innovations supporting mangrove conservation. Specifically, consumer-grade Unmanned Aerial Vehicles (UAV) were proven effective as potential remote sensing alternatives to support mangrove research and monitoring in recent studies. As most studies use custom UAV-mounted sensors for mangrove species classification, similar studies using a UAV’s default red–green–blue (RGB) cameras were scarce. This study explores the potential of high-resolution RGB aerial images through state-of-the-art object detection algorithm, YOLOv5 to detect the dominant Rhizophora mangroves in Sarawak, Malaysia. A total of 400 RGB images were equally selected from two study areas and allocated into three datasets, two corresponding to each study area and one combining all images. The annotation process was performed using a previously proposed novel method, assisted by YOLOv5 for a semi-automated annotation process with expert verification. Systematic training experiments were conducted to select an optimal epoch size across models trained with each dataset. The final models produced an average true positive rate of 73.8% and 71.7% for each study site, while the combined dataset model produced an average true positive rate of 73.7%. Overall, this study demonstrated the potential of UAV-based RGB images and deep learning object detection architectures to identify specific mangrove objects, while also highlighting key considerations for similar future research.