Virtually all marine conservation planning and management models in place or proposed have in common the need for improved scientific rigor in identifying and characterizing the marine habitats and processes encompassed. An emerging central theme in the last few years has been the concept of representativeness, or representative systems of marine protected areas (MPAs). Representativeness and similar terms are used in two distinct senses in current literature, leading to considerable confusion. Definitions of these terms as they are currently used are provided. The habitat classification and mapping needed to incorporate considerations of representativeness into MPA planning must logically be carried out at the same scale at which management occurs. Management of highly protected areas is found to occur almost exclusively at local scales or finer, independent of the reservation model or philosophy employed. Current techniques for cost-effective surveying of marine areas are discussed. The emerging field of remote videography, in some cases linked with acoustic discrimination sensors, can provide quantitative data on real biological distributions. Such data lend themselves well to robust multivariate analysis in deriving habitat maps at scales relevant to managers, as a basis for assessing and planning for representation in MPA design.