Understanding environmental factors that influence forest health, as well as the occurrence and abundance of wildlife, is a central topic in forestry and ecology. However, the manual processing of field habitat data is timeconsuming and months are often needed to progress from data collection to data interpretation. Computerassisted tools, such as deeplearning applications can significantly shortening the time to process the data while maintaining a high level of accuracy. Here, we propose HabitatNet: a novel method based on Convolutional Neural Networks (CNN) to segment habitat images of tropical rainforests.HabitatNet takes color images as input and after multiple layers of convolution and deconvolution, produces a binary segmentation of the input image. We worked on two different types of habitat datasets that are widely used in ecological studies to characterize the forest conditions: canopy closure and understory vegetation. We trained the model with 800 canopy images and 700 understory images separately and then used 149 canopy and 172 understory images to test the performance of HabitatNet. We compared the performance of HabitatNet with a simple threshold based method, a manual processing by a second researcher and a CNN approach called UNet upon which HabitatNet is based.HabitatNet, UNet and simple thresholding reduced total processing time to milliseconds per image, compared to 45 seconds per image for manual processing. However, the higher mean Dice coefficient of HabitatNet (0.94 for canopy and 0.95 for understory) indicates that accuracy of HabitatNet is higher than that of both the simple thresholding (0.64, 0.83) andUNet (0.89, 0.94). HabitatNet will be of great relevance for ecologists and foresters, who need to monitor changes in their forest structures. The automated workflow not only reduces the time, it also standardizes the analytical pipeline and, thus, reduces the degree of uncertainty that would be introduced by manual processing of images by different people (either over time or between study sites). Furthermore, it provides the opportunity to collect and process more images from the field, which might increase the accuracy of the method.Although datasets from other habitats might need an annotated dataset to first train the model, the overall time required to process habitat photos will be reduced, particularly for large projects.