The ability of a researcher to re-identify (re-ID) an individual animal upon re-encounter is fundamental for addressing a broad range of questions in the study of ecosystem function, community and population dynamics, and behavioural ecology. In this review, we describe a brief history of camera traps for re-ID, present a collection of computer vision feature engineering methodologies previously used for animal re-ID, provide an introduction to the underlying mechanisms of deep learning relevant to animal re-ID, highlight the success of deep learning methods for human re-ID, describe the few ecological studies currently utilizing deep learning for camera trap analyses, and our predictions for near future methodologies based on the rapid development of deep learning methods. By utilizing novel deep learning methods for object detection and similarity comparisons, ecologists can extract animals from an image/video data and train deep learning classifiers to re-ID animal individuals beyond the capabilities of a human observer. This methodology will allow ecologists with camera/video trap data to re-identify individuals that exit and re-enter the camera frame. Our expectation is that this is just the beginning of a major trend that could stand to revolutionize the analysis of camera trap data and, ultimately, our approach to animal ecology.