Protected marine areas management depends mainly on the zonification schemes applied. The aim of the present work is to propose a zonification scheme for protected marine areas in the coastal zone, based on the ecosystem features. This ecosystemic zonification is based on structural and functional elements of marine ecosystems, and allows the incorporation of the main environmental characteristics into the management plan of these areas, whether information about biotic factors is available or not. Based on this, a zonification of the Sistema Arrecifal Veracruzano National Park is proposed, which considers the identification of various subsystems, seascapes and environmental units within nested scales, to be included in the national park management plan.