A new approach was applied to mapping out the reef substrate of the four islets of Pulau Payar Marine Park, in Kedah State, Malaysia. A seabed classification system which harnessed the RoxAnn hydroacoustic signal processor, Differential GPS and a 200 kHz echosounder was able to translate the echo return into hardness and roughness indices, which then exhibited unique characteristics for each bottom type recorded. The system was able to discriminate six major reefsubstrates i.e. live coral, dead coral, soft coral, coral rubble, rock and sand. Live hard coral represents a total coverage of 19.30% from the 157.68 km total length of transect recorded from the Payar group of islands. The four main growth forms found were the massive (10.11%), the branching (7.11%), the encrusting (1.51%) and the foliose (0.57%). Table corals and columnar corals were also present but in a very small quantity (surface area) — the RoxAnn seabed classification system was not able to classify them as a separate group. As for the Pulau Segantang group ofislands, soft coral was the dominant coral type, accounting for 34.65% of the total 4.12 km of track run. Live coral coverage at P. Segantang in this survey was negligible. It was also common to find small coral colonies growing on the boulderssurface in shallower waters for both Payar and Segantang waters. They were grouped as a stand-alone coral substrate due to their unusual existence pattern. The real time trace data were also interpolated using Surfer®6.2 for thematic maps showing the depth contour, the 3D depth profile and the bottom surface area. The results were satisfactory, despite data distortion. The use of the hydroacoustic method for themapping of coral reef substrate is independent of water depth, visibility, light penetration and time. Hence, the hydroacoustic method shows itselfto be a better alternative to the conventional transect line method and satellite images in terms of time and cost spent and the results gained especially for large-scale surveys.