Kenya’s natural resource base has dwindled over years. The existence of many natural resource policies, some that are incompatible, has resulted in complex rangeland management regimes, giving rise to fragmented interventions and inadequate natural resource policies in relation to pastoralism. The majority of pastoral land resources held under a controlled access system by the national government that regulates management and utilization of resources. Pastoralists in Kenya have become among the most marginalized and disadvantaged minority groups. This is due to limited or under investment by government and other actors, and access to, or ownership of land, water and other resources, which are fundamental for pastoralism. This study examines significant obstacles for the establishment of a more inclusive ‘governance’ approach to natural resource management in northern Kenya, that characterize the customary Boran knowledge such as Deedha’s (traditional grazing unit) and formal institutions and seeks to address the tension between them through a legal framework that accommodates both. The results of the study established existence of the traditional structures and institutions in governance of natural resources within the pastoralist communities in Isiolo County. These institutions have evolved to cope with changing dynamics brought about by formalization of the natural resources governance. The resulted showed that various formal institutions from national government agencies to county government department were involved in management of the natural resources. However, the study established various operational divergence and links between informal and formal institutions involved in natural resources management. The study concluded that both informal institution such as Deedha and formal institutions constituted by national and county government did governance of natural resources among pastoralist communities in Isiolo County. The communities however have more trust in the informal structures and institutions because of their flexibility and inclusiveness.