The history of the Department goes back as far as 1863 when by virtue of a Spanish Royal Decree an office known as Inspeccion General de Montes was created in the Philippines. Although that agency focused on forest administration in its generic terms as dictated by the limited scope of services then required, nevertheless its functions and responsibilities included several concerns related to the management of a wide range of natural resources, such as forest inventory and protection, land classification, watershed protection, water, biodiversity and mineral resources conservation.

In 1901, the Department of Interior was created vested with the powers and authority on matters that included natural resources. The Department of Interior continued to exist for about 15 years until November 18, 1916 when Act No. 2666 was enacted. The act entitled "An Act to Reorganize the Executive Department of the Government of the Philippine Islands" abolished the Department of Interior and transferred its functions and authority to the Department of Agriculture and Natural Resources (DANR).

Under Act 2666, the DANR took "direct executive control, direction and supervision of the Bureau of Agriculture, Bureau of Forestry, Bureau of Lands, Bureau of Science and the Weather Bureau and all matters concerning hunting, fisheries, sponges and other sea products and such others as may be hereafter assigned to it by law". The Bureau of Science was the result of the merger of the Mining Bureau and the Bureau of Government Laboratories.

In 1932, a new reorganization act was passed, providing for the renaming of DANR to Department of Agriculture and Commerce (DAC) and the addition of another bureau to it - the Bureau of Commerce. It was also at this time that the Bureau of Agriculture was split into the Bureau of Plant Industry and the Bureau of Animal Industry. This raised to seven the number of bureaus in the former DANR.

A year later, by virtue of the same Act, the following entities were organized and placed under the direct control and supervision of the Secretary of Agriculture and Commerce: Divisions of Accounts and Property, Statistics and Publications, Mineral Resources, Industrial Engineering, Home Economics and Navigation, Fish and Game Administration, Fiber Inspection Service and Scientific Library Division.

During the period 1934 to 1938, the Divisions of Mineral Resources, Industrial Engineering and Home Economics, Fish and Game Administration and Scientific Library Division were placed under the Bureau of Science while the Division of Accounts and Property was abolished. One highlight of this same period was the creation of the Bureau of Mines (out of the erstwhile Division of Mineral resources) by virtue of Commonwealth Act No. 136.

From 1938 up to the outbreak of the Second World War in 1941, other organizational changes took place. The Fish and Game Administration was divided. The functions relating to fish and fisheries went to the Division of Fisheries under the Office of the Secretary of DAC while those relating to game administration went to the Bureau of Forestry. A new division called the Division of Soil Survey was created under C.A. No. 418 to undertake soil and agronomical survey and placed under the Office of the Secretary. The Division of Statistics and Publications rose to become the Bureau of Census and Statistics under the Office of the President. The Office of the Secretary was reorganized into 3 divisions, namely: Administrative, Legal and Technical Divisions. The Natural History Museum Division was transferred from the Bureau of Science to the Office of the Secretary.

After the war, on July 1, 1945, the DAC was reconstituted on account of the changes made by the Philippine Republic. A reorganization act in 1947 brought back the name Department of Agriculture and Natural Resources but transferred the Bureau of Commerce and Weather Bureau to a new Department of Commerce and Industry. The Divisions of Fisheries and Natural History Museum were transformed into bureaus and were placed under the Office of the President.

An enabling act in 1953 added the Bureau of Agricultural Extension to the DANR. On this same year, the Office of Agricultural Information was established.

There were no major changes in the DANR's structure from 1954 to 1974. However, the end of DANR came on May 17, 1974 when Presidential Decree No. 461 was issued providing for the Department\'s reorganization into 2 departments, namely: the Department of Agriculture (DA) and the Department of Natural Resources (DNR).

Under this set-up, the DNR took the following line bureaus and attached agencies: Bureau of Forest Development (BFD), Bureau of Mines (BM), Bureau of Lands (BL), Bureau of Fisheries and Aquatic Resources (BFAR), National Committee for Mineral Exploration and Survey Operations (NACOMESCO), Presidential Committee on Wood Industries Development (PCWID), Fishery Industry Development Council (FIDC), Surigao Mineral Reservations Board (SMRB) and the Presidential Action Committee on Land Problems (PACLAP).

Certain agencies were created later on and attached to the DNR. These were the Forest Research Institute (FORI) established on December 8, 1974 under PD No. 607; the Philippine Fish Marketing Authority (PFMA), on August 11, 1976 under PD No. 977; the Natural Resources Management Center (NRMC), on October 25, 1976 under PD NO. 1041; the National Environmental Protection Council (NEPC), on April 18, 1977 under PD No. 1121; and the Mineral Reservation Development Board (MRDB) taking over the functions and powers of the abolished SMRB on February 1978 under PD NO. 1305.

With the shift to a parliamentary form of government in 1978, the DNR became the Ministry of Natural Resources (MNR). A component arm, the Natural Resources Development Corporation was started under Executive Order No. 786 in 1982.

In 1985, the concern on fish and fisheries was transferred to the Ministry of Agriculture, leaving the MNR with only three (3) bureaus aside from the attached entities.

On January 30, 1987, Executive Order No. 131 was issued creating the Department of Energy, Environment and Natural Resources (DEENR) that took the powers and functions of the MNR and embraced the emerging critical concerns about energy and environment. However, EO 131 was never implemented. Executive Order No. 192 came out on June 10, 1987, reorganizing the DEENR and renaming it as the Department of Environment and Natural Resources (DENR).