The biological diversity of the Chilean marine ecosystem (CME) has recently become an issue of interest to Chilean scientists and authorities concerned about the impact of human activities and ongoing climate change on the structure, functioning, and sustainable use of this large marine region, recognized as one of the most productive ecosystems of the world`s is oceans. In this paper, the available information is examined in order to describe the major environmental characteristics of the CME and its associated flora and fauna, both in the benthic and pelagic systems, with the main goal of identifying environmental discontinuities and boundaries which may serve to define biogeographical units and characterize their biodiversity patterns. Physical and chemical processes are also described. In the pelagic system, three major regions may be identified: (1) the Northern Upwelling Region (18º-30º S), (2) the Central/Southern Upwelling Region (30º-42º S), and (3) the Austral Fjords Region (42º_55ºS). These could be defined as biogeographical units, though biodiversity patterns may still require further analyses. For the benthic system, two major provinces are distinguished: the Peru-Chile province (from Paita in Peru to Valparaíso in Chile) and the Magellanic province (Chiloé Island to Cape Horn). A clear transition zone at about 30ºS has also been described. The limits of these biogeographical regions, however, are not fixed and may vary seasonally and interannually. Diversity patterns, as well as dominant and key species inhabiting these biogeographic compartments, are described on the basis of the available data. The studies now required to obtain better information to describe diversity and to identify the underlying processes are stressed, as well as the needs for initiating large scale and long-term programs for monitoring species and processes in the CME that may allow future analyses of diversity patterns along the Chilean coast for conservation purposes.