Seagrass beds play an important role in coastal ecosystems as primary producers and providers of habitat and environmental structure. Therefore, mapping seagrass beds is indispensable in the management and conservation of sound littoral ecosystems, and in the development of sustainable fisheries in coastal waters. Multi-beam sonar is often used to map bottom topography. We developed a mapping method to quantify the volume of seagrass using a multi-beam sonar. Seagrass beds were scanned with the multi-beam sonar and quadrat sampled to verify the distribution of seagrasses. We used software to discriminate seagrass signals from echoes to obtain a topographic profile of the bottom without seagrass; this was then subtracted from the topography including the seagrass. We then mapped seagrass distribution, calculated seagrass volume, and estimated biomass using volume and quadrat samples. We applied these methods to map a seagrass bed of Zostera caulescens in Otsuchi Bay, on the Sanriku Coast of Japan, during the growing season of 2001. A transducer was attached to a boat (one gross ton) equipped with a differential-GPS, a motion sensor, and a gyrocompass. The vessel completed a grid survey scanning whole seagrass bed with an area of 115 m × 156 m at bottom depths between 2 and 8 m within about 40 min when traveling at a speed of 1.5 m s–1 (3 knots). The multi-beam sonar was able to visualize three-dimensional seagrass distribution without interpolation and easily to estimate area and volume occupied by the seagrass using hydrography software. The results indicated that Z. caulescens was distributed at bottom depths of 6–7 m with a surface area of 3 628 m2 and a volume of 1 368 m3. The mean biomass of above- and below-ground parts of seagrass were estimated to be 28.6 gDW m–2 (range 26.6–30.9) and 15.9 gDW m–2 (range 14.1–17.7). Our study demonstrated that multi-beam sonar is effective for mapping and quantifying the spatial distribution of seagrass beds, and for visualizing the landscape of the seagrass canopy.