Feel free to post links to projects you're aware of using Deep Learning to assist in conservation.
Here's a few to get started.
Classification of 121 Plankton species from underwater imagery. The winning entry, and many of the top entries, used deep-learning based approaches.
Identification of Right Whale individuals from aerial imagery. Many of the leading entries are using deep learning
Deep Learning for Large Scale Biodiversity Monitoring. Paper from Conservation Metrics, Inc. (I'm an author) describing their use of Deep Learning for bioacoustic and camera trap monitoring of endangered seabirds, invasive snakes, and more.