Conservation efforts use scientific data to provide an adaptive framework wherein habitat and wildlife sustainability can co-exist with human activities. Good science informs decision-makers and facilitates the development of successful conservation approaches. However, conservation concerns for the dugong Dugong dugon in South-east Asia are sufficiently urgent that action must be taken quickly, even though science has not provided complete answers to critical questions. In Johor, Malaysia, aerial surveys were conducted to assess dugong numbers, dugong high-use areas and overlap of dugong sightings with areas of seagrass. Dugong distribution included existing marine parks and locations where known conservation threats exist. We conclude that the Johor islands may represent a significant congregation site for dugongs in Peninsular Malaysia, with as many as 20 dugongs recorded in a single day. The existence of a marine park where the dugong sightings were most prominent is encouraging but only 38% of those sightings fell within the boundaries of the park. Anthropogenic threats need to be assessed and addressed prior to complex development activities such as dredging and coastal reclamation for tourism development in this critical area. We use this case to explore the concept of advancing species conservation through focused research and management, particularly where uncertainties exist because data are scarce.