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The last decade has transformed the field of artificial intelligence, with deep learning at the forefront of this development. With its ability to ‘self-learn' discriminative patterns directly from data, deep learning is a promising computational approach for automating the classification of visual, spatial and acoustic information in the context of environmental conservation. Here, we first highlight the current and future applications of supervised deep learning in environmental conservation. Next, we describe a number of technical and implementation-related challenges that can potentially impede the real-world adoption of this technology in conservation programmes. Lastly, to mitigate these pitfalls, we discuss priorities for guiding future research and hope that these recommendations will help make this technology more accessible to environmental scientists and conservation practitioners.