Collaborative governance strengthens the relationship between different beneficiaries in line with up-bottom approach to natural resources management. Social capital is one of the major components contributing to the collaborative governance of natural resources. Accordingly, the level of social capital of local beneficiaries was investigated both prior and post collaborative project implementation through the measurement of trust and collaboration ties as well as the measurement of whole network quantitative and mathematical indexes (density, reciprocity, transitivity, and Geodesic distance). Present study was carried out in AsadAbad Sofla village in Abarkuh district of Yazd province as a part of carbon sequestration project. It was revealed that all above-mentioned indexes increased following project implementation during two years (from 2014 until 2016. Density of trust and collaboration ties increased hugely. In other words, bonding social capital enhanced. Consistency and the balance of network was average pre-project implementation but these indicators increased to higher levels. The unity of beneficiaries increased significantly and considerable improvement in trust ties was observed. Therefore, following the implementation of carbon sequestration project, trust building and reinforcement of cooperation occurred and bonding social capital strengthened which left positive effects upon the collaborative governance of natural resources.