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The “Coastal and Marine Ecological Classification Standard (CMECS)”, a new approach to ecological classification, was applied to 122 km of the southern intertidal zone of Qeshm Island located the Hormouz Strait - the Persian Gulf. Two components of this model, Surface Geology (SGC) and Biotic Cover (BCC) were used. Considering the extent and geomorphological alternations of the covered area, 12 sampling sites within 5 sub-regions were designated using by GPS. In total, 60 habitats (biotopes) with 47 codes were determined; this variety of biotopes is directly related to the diverse surface geology (substrate) of the covered area. Most of the biotopes and codes were recorded in the mid-eastern coastal zone, due to heterogeneity in substrate structure associated with numerous ecological niches in rocky shores. Crustacean species such as Eriphia smithi, Thalamita prymna, Molluscan species such as Clypeomorous bifisciatus, Cerithium caeruleum and echinoderm species such as Echinometra mathaei and Ophiactis sp. were characteristic of rocky shores, while Crustacea groups including Ocypode rotundata and Dotilla sp., and Umbonium vestiarium (Mollusca) were characteristic of sandy shores. Although the highest number of codes was recorded in Zeitun Park site (Eastern coast), it did not possess the expected specific species (such as Diadema setosum, Linckia multiflora and Ophiocoma scolopendrina), that were encountered in sites with similar surface geology. This could have been caused by tourist traffic at the Zeitun Park site.