This paper describes a tracker specially designed to track clicking beaked whales using widely spaced bottom-mounted hydrophones, although it can be adapted to different species and sensors. The input to the tracker is a sequence of static localization solutions obtained using time difference of arrival information at widely spaced hydrophones. To effectively handle input localizations with high ambiguity, the tracker is based on multi-hypothesis tracker concepts, so it considers all potential association hypotheses and keeps a large number of potential tracks in memory. The method is demonstrated on actual data and shown to successfully track multiple beaked whales at depth.