Coral reef ecosystems are some of the diverse and valuable ecosystems on earth. They support more species per unit area than any other marine environment and are essential to the sustenance of life in our oceans. However, due to climate change, only under 46% of the worlds coral were considered healthy as of 2008. One of the biggest challenges with regard to coral conservation is that reef mapping is currently carried out manually, with a group a divers manually moving and placing a large PVC quadrat for every unit area of the reef and then photographing and analyzing each unit separately. Hence, there is a pressing need to improve the methodology of imaging, stitching and analyzing coral reef maps in order to make it feasible to protect them and sustain life in our oceans. To improve the current methodology, a reef-mapping surface drone robot which photographs, stitches and analyzes the reef autonomously was built. This robot updates the physical quadrat which is used today, to a projected laser quadrat, which eliminates the need to dive to the bottom of the sea and allows relative pose estimation. The robot then captures and processes the images and using 3D reconstruction and computer vision algorithms is able to map and classify the coral autonomously.