Blue carbon ecosystems (BCEs) are linked to tourism industry either as the main destination site or as additional features. Achieving sustainable tourism in coastal areas warrants the inclusion of long-term BCE management and protection, hence, it is important to understand how tourism impacts these resources to better formulate apt strategies tailored to the individual contexts. In Busuanga Island, Philippines, where tourism industry depends highly on its coastal and marine resources, there is a gap in understanding the impacts of tourism on BCEs. Thus, this study aims to analyze communities’ perceptions of sustainable tourism and BCE services by comparing household survey results between urban (Coron) and rural (Busuanga) communities. Specifically, this work aims to determine residents’ perceptions of tourism impacts at the personal and community levels, to examine whether socio-demographic profiles, ecological consciousness, awareness of programs for sustainable tourism, and ecological protection drive these perceptions, and to compare these results in urban and rural settings. Results of this study indicate a distinctive difference between urban and rural perceptions; e.g., residents perceived highly of tourism benefits and impacts in Coron whereas fewer recognitions are observed in Busuanga. Correlations of locals’ awareness of BCE services with perceived environmental changes caused by tourism showed positive effects. Environment-related plans received high recognition in promoting sustainable tourism. Overall, locals’ perceptions of tourism and blue carbon ecosystems can be bundled together. This linkage could address future planning of sustainable tourism master plan at the municipal level particularly those towns that features coastal resources as their main tourism attractions.