Marine invasive macroalgae alter the environment in which they settle, changing food chains, generating structural variations and, sometimes, displacing native species. Halimeda incrassata (H.i.) is a tropical seaweed that settles mostly on sandy substrates and that has expanded almost sevenfold in the Balearics from 2011 to nowadays. Measuring its coverage is crucial to estimate its expansion rate and plan effective eradication actions. In the last years, the Marine Robotics team of the Systems, Robotics and Vision group (University of the Balearic Islands) has collaborated actively with biologists in the observation of sensible marine habitats using an Autonomous Underwater Vehicle to get data and image processing techniques to infer information of biologic interest. Several marine areas of Cabrera National Park were surveyed by our robot for H.i. video recording. Images of videos were used to form photo-mosaics, mark all H.i. shoots and calculate automatically its coverage with software. Time, extension and depth of data collection campaigns increase, offering measurements more accurate, and with higher temporal and spatial resolutions than those obtained with traditional techniques based on divers and quadrat frames.