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Abstract Loss of marine biodiversity through benthic habitat destruction has created urgent needs for low-cost, high-performance seafloor survey methods. However, accurate seafloor mapping and classification is usually an expensive undertaking requiring sophisticated equipment, which excludes important low-budget user groups in developing nations. In this paper, we introduce a low-cost procedure for seafloor mapping based on free-of-charge data acquisition software that can be downloaded from the Internet. Using a Malaysian coral-reef case-study, we show how comprehensive bathymetric mapping can be implemented with such software using inexpensive eccosounder and GPS, and describe principles for integration of environmental data, either by connecting additional instruments to the computer (up to 32 instruments with up to eight channels each can be handled simultaneously), or by using simple synchronisation techniques with equipment that records to separate media, such as video cameras. We mapped a Malaysian coral-reef area of 114 hectares in 6 hours of video mapping, achieving reef mapping rates that matches rates currently achieved only with air-borne imaging devices. However, the present methodology results in completely ground-truthed data that can be classified according to many schemes by direct observation of the habitat, and provides detailed bathymetric data that satellite imagery or air-borne spectrographic sensors do not provide.

The method can be used as a stand-alone reef mapping and classification tool on the scale of tens to hundreds of square kilometres. On larger scales (thousands of square kilometres), airborne survey methods are likely to remain more cost-effective than boat-based methods, yet also in such settings this simple method offer unprecedented capacity for ground truthing and thereby increased capacity for habitat classification.