Instance segmentation dataset created for the research 'Monitoring Mammalian Herbivores via Convolutional Neural Networks implemented on Thermal UAV imagery'. It comprises 959 frames, 20.647 masks, and 239 tracks, and consists of 7 video sequences depicting aerial thermal imagery of cattle collected with a UAV (Parrot ANAFI Thermal) in two outdoor farms in the Netherlands. Data were acquired at three temperatures (10ºC, 19ºC, and 26.5ºC), under sunny and overcast weather conditions, at various angles of inclination (including nadir), and at heights ranging between 8-28 meters. Ground truth was labeled manually with the Computer Vision Annotation Tool CVAT.