Coastal habitats and shoreline regions are considered the most valuable marine areas due to their special importance in terms of conservation, tourism, natural attractions, and environmental significance. The classification of marine habitats constitutes a component of research that defines various discrete habitat types within a spatial scale. The primary objective of this classification is to provide a unified language through which habitat-related data and information can be communicated and managed effectively. Konarak and Pozm Bays possess high ecosystem and habitat diversity, which underscores their ecological importance. The aim of this study is to delineate the ecosystem boundaries and dominant geomorphic features of each region using the CMECS classification method. The classification of coastal habitats in Konarak and Pozm Bays was conducted using the latest version of the CMECS system. Through field surveys along the coastal strip of each area and based on geomorphological features, sub regions were identified and defined. Following the classification protocol, the coastal belt was considered from the subtidal zone up to the supratidal (spray) zone. Based on the analysis of CMECS classification parameters and geological codes, all coastal habitats in both Pozm and Konarak Bays fall within the marine system, the intertidal and subtidal zones, and the nearshore subsystem. Examination of the surface geological component, aimed at determining whether substrates originate from biogenic or geological sources, showed that the defined subclasses belong to rocky substrates and unconsolidated substrates, represented by six distinct codes in total. The analysis of surface geological codes in the coastal zones of Pozm and Konarak indicates that all shorelines possess geological origin, and none of the areas is classified as substrates formed by biological activity. Furthermore, the entire study area, at the level of natural geographic units, falls within the continental shelf or island category. Accordingly, the natural geoforms identified in the coastal zone include sandy flats, rocky sections, tidal channels, and tidal pools, which reflect the high diversity of geomorphological features and the applicability of the CMECS method in identifying and characterizing these attributes. This study represents the first use of this model along this segment of the Makran coast; therefore, the method and its outcomes may be of significance to other researchers and marine-related institutions. Moreover, compared with previous versions, the cumulative modifications appear to have substantially improved the usability of the current version. The distinctiveness of the various CMECS components is such that each represents a specific aspect of marine and coastal environments, while they can also be combined for mapping purposes. Thus, this coding system facilitates communication between researchers, scientific communities, and resource managers, serving as a shared standard for data organization. Additionally, the dynamic and continuously updated nature of CMECS, informed by its application in marine environments worldwide, will contribute to its ongoing improvement. Using this model in our study is also the first attempt conducted in this part of the Makran coasts; therefore, the method and its results may be of considerable importance to other researchers as well as institutions involved in marine sciences and marine management.