Delimiting urban sprawl boundaries have been generally regarded as a regulatory policy measure to control chaotic and sparse urban expansion and for the protection of ecological areas towards sustainable development. The conservation of ecologically sensitive areas plays a key role in environmental protection; so, harmonizing urban sprawling with nature conservation can be viewed as a binary compatibility planning problem. This study aims to employ a geographical allocation model, based on the minimization of the environmental cost in order to apply complex spatial clustering techniques. Firstly, five ecological sensitivity factors affecting the ecological footprint of the study area are modeled through Geographic Information Systems (GIS) and Analytic Hierarchy Process (AHP) method in order to evaluate the Ecological Sensitivity Index. Then, several spatial objectives and constraints such as distance from the shoreline, continuity, and compactness are applied and finally, the most optimal areas are extracted for future urban sprawl. Spatial regulations, siting rules considerations and scenarios based on the parameters of the spatial clusters outputs are tested to the commune of Mytilene, located on Lesvos Island, Greece, where strong land use changes have been recorded by the urban sprawl over the last three decades.