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Anthropogenic habitat destruction and climate change are reshaping the geographic distribution of plants worldwide. However, we are still unable to map species shifts at high spatial, temporal, and taxonomic resolution. Here, we develop a deep learning model trained using remote sensing images from California paired with half a million citizen science observations that can map the distribution of over 2,000 plant species. Our model—Deepbiosphere—not only outperforms many common species distribution modeling approaches (AUC 0.95 vs. 0.88) but can map species at up to a few meters resolution and finely delineate plant communities with high accuracy, including the pristine and clear-cut forests of Redwood National Park. These fine-scale predictions can further be used to map the intensity of habitat fragmentation and sharp ecosystem transitions across human-altered landscapes. In addition, from frequent collections of remote sensing data,Deepbiospherecan detect the rapid effects of severe wildfire on plant community composition across a 2-y time period. These findings demonstrate that integrating public earth observations and citizen science with deep learning can pave the way toward automated systems for monitoring biodiversity change in real-time worldwide.