Through Indigenous Protected Area (IPA) planning seagrasses have been identified by Wuthathi people as a significant value of Country in need of monitoring and protecting for future generations. The Wuthathi people are Traditional Custodians for northeastern Cape York Peninsula including 8,072 km2 of marine waters within the Great Barrier Reef which contains 9 out of the 15 species of seagrasses found in Queensland. The IPA plan provides the vision for the management of Country and the types of partnerships needed to support this. Within this planning context the Wuthathi Aboriginal Corporation and James Cook University (JCU) began co-designing a seagrass monitoring program with Elders, Custodians and seagrass scientists. Through this project we have strengthened our relationship with JCU, extended our knowledge of seagrasses within Wuthathi karakara and mapped previously unrecorded seagrass beds. This project exemplifies the benefits (social, cultural, and environmental) that can be achieved through collaborative partnerships when lead by First Nations. A major challenge to establishing and continuing our seagrass monitoring project and partnership with JCU is the siloed, short-term, grant based and bureaucratic nature that funding is made available to First Nation people, which is a major barrier to continuing long term monitoring and management.