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Nepalese agriculture sector has undergone through several restructuring process in past few decades. In this context, three separate departments for Agriculture, Livestock Services and Central Food Research Laboratory were established from current Department of Agriculture Development in 2052 B.S. Realizing the importance of cereal crop, lentils and  industrial crops separate Crop Development Division was established under Department of Agriculture in 2052 B.S.  It's major objective was to conduct programs for farmers in district level, coordinate and cooperate with the concerned stakeholders in central level and to develop policy and guidelines at the national level. Later on, in 2057 B.S. Crop Development Division was changed to Directorate of Crop Development continuing with the same functions and objectives. According to the modified structure of Department of Agriculture in 2060/61 B.S. National Industrial Crop Development Program and five Regional Seed Testing Laboratories were established under Directorate of Crop Development.

With the restructuring of the state, according to the Constitution of Nepal 2073 Center for Crop Development and Agro Bio-diversity Conservation was established to carry out the regular activities conducted by Directorate of Crop Development besides seed testing. In addition to this, it is further strengthened to provide the services for agro-biodiversity conservation. It is focal organization for developing national policy and procedures in area of agriculture biodiversity conservation. Two Agriculture Development Farms situated at Sundarpur and Chandradangi are kept under this center.