In this study, the role of cultural routes in the protection and promotion of cultural heritage context in rural areas is examined within the frame of sustainable and spatial development. The main objective is the development of an integrated strategic plan for the protection and promotion of cultural heritage, through the implementation of an innovative methodological approach for the organization and management of cultural routes, incorporating standardized processes with information technology. The proposed methodology is applied on two routes of natural and cultural importance in Chios Island. A Geographic Information System is used as a decision support tool. Spatial data consisted of digitized maps of the study areas, whereas attribute data consisted of in situ observations, featuring the current state of the sites, data from a previous study on the paths and procedures according to ISO 9001. Furthermore, Legal and Spatial Frameworks set the terms and directions on cultural and environmental protection and potential development factors. The comparison between the two elaborated thematic maps (current state and previous study) highlighted the problems related to the preservation state of the study areas: a small percentage of the proposed interventions in 1999 were implemented, whilst the routes have been left abandoned ever since. Additionally, the regions accept severe pressures and risks by growing urbanization tendencies. Final proposals for the protection and promotion of the study areas followed two levels of analysis: the routes and their environment, including conservation interventions and protection zones, as well as the organization of alternative tourism activities. As a result of the proposed study, it is shown that integrated planning through standardized procedures for the management of cultural routes as unified cultural systems, can contribute to the sustainable protection and promotion of cultural heritage in rural areas, offering economic development, social cohesion and cultural as well as the protection of natural resources.