Attaining sustainable resource management encompasses multilevel challenges and interdisciplinary approaches from grassroots efforts to international agreements. In the context of coastal and marine management, the complexities�represented by the variety of local entities, regimes, and institutional supports are captured as current challenges in sustainability efforts. Such challenges, unfortunately, persist in the group of customary communities such as those of the Bajau, who live in coastal and marine areas. In an effort to address the aforementioned challenges, this research proposes a model for integrating the Traditional Ecological Knowledge (TEK) of the Bajau into�Locally Managed Marine Areas (LMMA) scheme in Wakatobi, Southeast Sulawesi. A qualitative approach involving multi-sited ethnography and interviews was employed in this study. TEK as a concept is drawn upon to strengthen the local practices for sustainable resource use and therefore develop policy recommendations. However, in the case of Bajau communities, the dimensions of the TEK encompass conservation practices, ethno-fisheries, cultural beliefs, customary laws, weather and cultural astronomy, and adaptive management. The manifestation of the TEK needs to add the term 'exchange knowledge' due to the history and nature of former nomadic groups that interacted and exchanged knowledge and goods with other groups with whom they were in contact. Intercultural relations between the Bajau and dominant customary groups in Wakatobi position the Bajau as migrants and second-class people, both socio-culturally and in the context of various conservation activities. The co-management programs that involve the Bajau do not seem to consider the basic needs and practices of this group in current sustainable resource management. This situation indirectly contributes to the marginalization and growing development threats for the Bajau in Wakatobi. In addition, the complexities in the realm of contemporary Bajau society are not adequately considered in Wakatobi's development priority programs. The culturally inclusive projects and LMMA model do not engage Bajau communities, even though this group is pivotal in nurturing marine ecology in alignment with multiple TEK practices and a maritime culture orientation. In brief, the output model of this research examines the various terms to disentangle the challenges in cultural identity, intellectual property and rights, capacity building, livelihood diversification, and communal space in the Bajau communities in Wakatobi. In advance of making recommendations to implement the model, this research explored key attributes related to Bajau customary institutions, local government, and Wakatobi National Park.�