The Philippines has one of the most diverse seagrass meadows in south-east Asia, with substantial dugong populations still existing. However, the seagrass population is declining worldwide, and 30–40% of the seagrass areas in the Philippines have been lost in the last 50 years. The quadrat method by scuba diving has been widely used to study seagrass distribution and measure dugong feeding trails. However, this method is affected by observational skills of the divers and the survey time is usually limited by air capacity in the tank and effort for high-resolution sampling. In this study, a new method of seagrass mapping and quantification of dugong trail distribution is proposed and tested. The method produces clear and high-resolution data using acoustic and optical devices with high efficiency. The field study was conducted at Mayo Bay, southeastern Philippines. Continuous optical images were taken using a water-proof digital still camera from the sea surface by a swimmer with snorkel. Using the software PhotoScan, 3D optical images were generated from the continuous photos. The resolution of the optical image is 2.96 ± 0.17 (SD) mm per pixel so that a leaf of Halophila sp. is identifiable. By counting the pixels of dugong trails, the feeding rates were calculated and the values were 13.5% in the survey area 1 and 7.1% in area 2. The quantification method, based on high-resolution optical image generated by continuous photos, can be useful for assessing the status of the seagrass meadows and the distribution of dugong trails.