Background: "habitat classification models" are invaluable tools for species conservation, land-use planning, reserve design, and meta-population assessments, particularly at broad spatial scales". Globally, there are at least 23 schemes developed for habitat classification schemes. The pioneer attempts in Egypt for classifying habitats were started by the series of Kassas giving a concern about dry lands and desertification problems. The main purpose of this paper is to: 1) present a suitable model for large scale planning to support the decision making process towards the natural resources in Egypt, 2) standardize data collection on habitats which will assist in management and conservation of the Egypt's natural heritage.Results: This paper presents new GIS-based habitat classification hierarchy that contains 5 main habitat systems, 12 habitat sub-system and 36 habitat classes. One of the major outputs of this present scheme is to define the boundaries of the three classes (epipelagic -mesopelagic -bathypelagic) of the pelagic sub-system. Conclusion: This hierarchy represents a new GIS-based standardized habitats scheming for Egypt. It was designed to support the current efforts to define the key biodiversity hotspots as well as long term planning of biodiversity at the national level. This new habitat mapping/scheming, has considerable potential utility for conservation priority setting for Egypt; it could be used to design and update the existing protected areas network; it could be used to evaluate the protected areas system representativeness, and climate change impacts studies. It is recommended to link habitat classification and mapping efforts in Egypt to regional and global approaches.
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