The ERDB has started operating under the new organizational structure . The new organizational structure is composed of the ERDB main office (ERD-MO) and six Research Centers (RCs).

The ERDB-MO is composed of five research divisions, namely: Forest Ecosystems Research Division (FERD), Coastal Zone and Freshwater Ecosystems Research Division (CZFERD); Urban Ecosystem Research Division (UERD), Technology Transfer Division (TTD), and Laboratory and Experimental Services Division (LESD). In addition to these, two non-technical divisions are: Planning and Management Information Services Unit (PMISU) and the Administrative, Finance and Management Division (AFMD).

For the ERDB RCs, the six centers are identified as : Watershed and Water Resources Research Center (WWRRC),) Land Management, Agroforestry and Upland Farm Technology Research Center (LMAUFTRC, Biodiversity, Coastal, Wetlands and Ecotourism Research Center (BCWERC), Mining and Degraded Areas Rehabilitation Research Center (MDARRC), Forest and Timber Resources Research Center (FTRRC), and Urban, Toxic Substances and Hazardous Wastes Research Center (UTSHWRC).

The functions of the ERDB-MO are: formulate, implement, coordinate and evaluate integrated research, development and extension agenda/programs on environment and natural resources (ENR) and other related cross-cutting concerns to address the needs of the various sectors in support of the thrusts and programs of the Department; conduct basic researches and develop standards, protocol and science-based technologies to address the needs of the different DENR Bureaus, end-users and stakeholders; provide technical assistance by developing and maintaining networks and linkages with DENR bureaus and offices, local and international institutions, other stakeholders and civil society; and perform other functions that may be assigned by higher authorities.

ERDB RCs are mandated to: formulate, implement and monitor and evaluate applied and action-oriented Environment and Natural Resources-Research, Development and Extension Programs/Activities/Projects (ENR-RDE PAPs) on the watershed, water resources, lands, agroforestry and upland farming systems, biodiversity, coastal areas, wetlands and ecotourism, mining and degraded areas, forests and timber resources and toxic wastes and management of hazardous wastes; pilot test and verify the standards and protocols developed by ERDB-MO; provide the latter feedbacks towards their improvement; conduct coordination and networking services with RDE stakeholders; and provide technical assistance and extension services on ENR technologies. Aurora S. Jose, PMISU