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This research was conducted during 2007-2008 with the main aim of classifying marine coastal habitats in Gwatr Bay located in Iran-Pakistan border, south east of Sistan-Blaluchetan Province. We used Coastal-Marine Ecological Standard Classification (CMECS) with three data layers covering water column, benthic cover classifier and geomorphology. Layers and habitats information were analyzed in a GIS environment and the indicator species were determined. WCC classification was done based on temperature, salinity and clarity classifiers for Ichthyoplankton communities. The result showed that two main seasonal habitats including spring habitat (spring, summer and winter) and fall habitat, affected by the monsoon season is present in the area. Also we considered particle size and total organic matter in sediment as classifiers for benthic habitats which indicated two different habitats based on distances from shore. Habitats were divided into unmixed macro-benthos community (polychaete) and mixed macro-benthos community including: Polychaete, Amphipoda and Gastropoda. The habitats were shown on digital GIS maps with their specific codes.