The Department of Environment and Natural Resources (DENR) has its beginning in the old Department of Agriculture and Natural Resources (DANR). In recognition of the broad and diversified concerns on natural resources and agriculture the DANR was split into two (2) Departments through Presidential Decree No. 46 in May, 1974. As such, the conservation, optimal utilization and exploitation of the country's natural resources and wealth became the mandate of the Department of Natural Resources (DNR).

With the shift to a parliamentary form of government in 1978, the DNR was renamed the Ministry of Natural Resources (MNR). In 1984, by virtue of Executive Order No. 967, the management of the fisheries sector through the Bureau of Fisheries and Aquatic Resources (BFAR) was transferred from the MNR to the Ministry of Agriculture.

 The events of February 1986 had also brought radical changes that altered the character of the MNR. First, President Corazon C. Aquino issued Executive Order No. 131 on January 30, 1987 creating the Department of Energy, Environment and Natural Resources or DEENR. However, it was reorganized into the present Department of Environment and Natural Resources in June 1987 under Executive Order No. 192 having under its umbrella the Forest Management Bureau, Land Management Bureau, Environmental Management and Protected Areas Bureau, the Mines and Geo-Science Bureau and the Ecosystems Research and Development Bureau.

 In 23 February 1995, the passage of Republic Act No. 7901 creating Region Xlll to be known as the Caraga Administrative Region resulted to the transfer of the province of Surigao del Sur from Region Xl to form part of the newly created Region Xlll.

 Also in 1995, with the passage of Republic Act No 7942, the Mines and Geo- sciences became an attached Bureau under the Office of the Secretary with the same status as the DENR Regional Office. It was followed suit in June 23, 1999 by the Environmental Management Bureau which also became an attached Bureau by virtue of Republic Act 8749 and which the Environmental Management and Protected Areas Service (EMPAS), Separating the Protected Areas from that office.

 In September 2001, President Gloria Macapagal Arroyo issued Executive Order No. 36 providing for the reorganization of the administrative regions in Mindanao purposely to accelerate social and economic development, improve public services and efficiency in local Governance. In the said Executive Order Region Xl was known as the Davao Region to be composed of four (4) Provinces and five (5) Cities while the provinces of South Cotabato and Sarangani and General Santos City were transferred under the jurisdiction of Region Xll otherwise known as the SOCSARGEN Region.