Scientific plant breeding activities have initiated in Iran since 1930 with establishing Agriculture school, Falahat by Ministry of Agriculture in Karaj. Cereal research was launched in 1930 through selection and breeding for domestic populations of wheat. The school was, later, joined to University of Tehran, and a new enterprise Company called Seed Improvement Institution was established in 1948 in same city. Increasing research fields and limited administration systems and offices in Ministry of Agriculture, encouraged establishing an institute with extensive legal force. Therefore, Seed and Plant Improvement Institute (SPII) was born upon the request of the Ministry of Agriculture and on the basis of a bill of law approved by the National Assembly and the Senate on 1959, which its headquarter was formally located in Karaj. 

By increasing the efficiency and effectiveness of research in the SPII, the organization was gradually changed and evolved so that several research departments were appeared in the frame of the organization. Which were:
Oil Seed Research Dep. (in 1969), Maize Research Dep. (in 1970), Horticulture Research Dep. (in 1971), Vegetable Research Dep. (in 1978), Pulses Research Dep. (in 1980), Physiology and Biotechnology Research Dep. (in 1983), and Genetic & Statistics Dep. (in 1983).

Gradually and because of shifting in importance of some crops and research subjects, and the need to further strengthen them, departments or offices of the SPII were separated and appeared as independent institute as:
Institute for Pistachio Research (1992), Dryland Research Institute (1992), Date Palm Research Institute (1993), Rice Research Institute (1994), Citrus Research Institute (1996), Cotton Research Institute (1997), Biotechnology Research Institute (1999), Seed and Plant Certification and Registration Institute (2003), and Horticulture Research Institute (2014).
At present approximately 309 faculty members are human resources of SPII in the headquarter of the institute and throughout the country in 34 research centers and 59 research stations whom perform annually more than 800 research projects in different fields.