The principles of creating a hierarchical system of units for zoning the coastal zone and the shelf of the world ocean by bionomic (ecosystem) features are discussed. The solution of a number of scientific and applied problems requires zoning of ecoregions (sea basins) at the regional and topological levels. A system of units is proposed, taking into account the zonal, deep and azonal features of ecoregions. The main initial unit of bionomic zoning is the underwater landscape. As an example of zoning at the regional and topological levels, the morphological structure of the landscapes of the three districts of the Japanese coastal region of the Sakhalin orogenic region of the Japan Sea is considered. The hierarchical system of units of bionomic zoning allows identifying landscapes-analogues. The applied value of which is the ability to predict the introduction of beneficial species and provide for the risk of invasion of harmful species.