The preferred procedure nowadays for benthic habitat mapping is combining marine acoustic and ground truthing methods, with the former ones tending to be the swath sonars, such as the Multi Beam Echo Sounders (MBES) and the Side-Scan Sonars (SSS). Both above acoustic systems, in conjunction with an extensive underwater video footage, were employed to map in detail benthic habitats in the marine area of Laganas Gulf in the National Marine Park of Zakynthos Isl., Greece, including key protected habitats such as P.oceanica beds and coralligenous formations. Object oriented seafloor classification was achieved taking advantage of the multi-layer information available, including the two individual frequencies of SSS and the MBES backscatter, angular response, and bathymetry data. The extracted statistical derivatives regarded: (1) textural analysis of the multi-frequency backscatter imagery, (2) angular range analysis of the MBES backscatter, as well as (3) application of various bathymetric indices. Those derivatives were classified individually or fuzzed together, to explore the rate of improvement when choosing one system or another and to investigate their best combinations and practices towards valid seafloor classification. Benthic habitat classification has been comprehended using the NATURA and EUNIS classification schemes to be compatible with the EU regulations.