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The state of Baja California Sur (BCS), Mexico, has a coastline of 2131 km with eight Protected Natural Areas (PNA) (33,075 km(2)) mainly located in the coastal zone. Here, we (1) review the current status of the diversity and distribution of coastal ecosystems in BCS, (2) assess the composition and coverage of these ecosystems in PNAs, and (3) identify coastal ecosystems of special interest for conservation. The combination of spatial analysis techniques was carried out using LandSat TM images and GIS processing, considering ecoregions and ecosystems in the coastal zone, as well as through the application of an ecosystem diversity index. In the BCS coastal zone, 11 ecosystems were identified: scrub, coastal water body, riparian, bare soil, halophyte, beach, salt flat, mangrove, salt marsh, coral reef, and seagrass. The ecosystem diversity in BCS results from the coastal features that differentiate the Pacific and the Gulf coasts. PNAs include 17 % of coastal ecosystems. Bahia Magdalena (Pacific) and Bahia Concepcin (Gulf of California), which are key for conservation (including mangroves and seagrasses), should be considered either for classification as PNAs or for inclusion in coastal management programs. The combination of remote sensing and GIS with biogeographic and ecosystemic approaches in our study enabled to determine ecosystem diversity and set coastal conservation priorities in Baja California Sur, Mexico. Specifically, coastal ecosystems that are not currently included within PNAs and which should be considered as conservation priorities were identified.