Detecting animals to estimate abundance can be difficult, particularly when the habitat is dense or the target animals are fossorial. The recent surge in the use of thermal imagers in ecology and their use in animal detections can increase the accuracy of population estimates and improve the subsequent implementation of management programs. However, the use of thermal imagers results in many hours of captured flight videos which require manual review for confirmation of species detection and identification. Therefore, the perceived cost and efficiency trade-off often restricts the use of these systems. Additionally, for many off-the-shelf systems, the exported imagery can be quite low resolution (<9 Hz), increasing the difficulty of using automated detections algorithms to streamline the review process. This paper presents an animal species detection system that utilises the cost-effectiveness of these lower resolution thermal imagers while harnessing the power of transfer learning and an enhanced small object detection algorithm. We have proposed a distant object detection algorithm named Distant-YOLO (D-YOLO) that utilises YOLO (You Only Look Once) and improves its training and structure for the automated detection of target objects in thermal imagery. We trained our system on thermal imaging data of rabbits, their active warrens, feral pigs, and kangaroos collected by thermal imaging researchers in New South Wales and Western Australia. This work will enhance the visual analysis of animal species while performing well on low, medium and high-resolution thermal imagery.