Scientific plant breeding activities have been initiated in Iran since 1930, with establishing Agriculture School, Falahat, by the Ministry of Agriculture in Karaj. Cereal research was launched in 1930 through the selection and breeding in native wheat populations and landraces. The school was, later, joined to the University of Tehran, and a new enterprise called the Seed Improvement Institution was established in 1948 in Karaj. Increasing research fields and limited administration systems and offices in the Ministry of Agriculture necessitated the establishment of an institute with extensive legal commitments.
Therefore, the Seed and Plant Improvement Institute (SPII) was born on the basis of law passed by the National Assembly and the Senate in 1959 by the Ministry of Agriculture, and its headquarter was formally located in Karaj. By increasing the efficiency and effectiveness of research achievements of the SPII, the institute gradually developed and different research departments were formed: Oil Seed Research Department (in 1969), Maize Research Department (in 1970), Horticulture Research Department (in 1971), Vegetable Research Department (in 1978), Pulses Research Department (in 1980), Physiology and Biotechnology Research Department (in 1983), and Genetic & Statistics Department (in 1983). 

Gradually, due to changes in the importance of some crops and research fields, and the need to strengthen them, some research departments of the SPII were separated and became independent institutes, e.g., Pistachio Research Institute (1992), Dryland Agriculture Research Institute (1992), Date Palm Research Institute (1993), Rice Research Institute (1994), Citrus Research Institute (1996), Cotton Research Institute (1997), Agricultural Biotechnology Research Institute (1999), Seed and Plant Certification and Registration Institute (2003), and Horticulture Research Institute (2014). Currently, more than 185 faculty members are conducting research projects at the headquarter of the institute and 25 provincial agricultural and natural resources research and education research centers throughout the country in 46 research field stations. They conduct more than 671 experiments/locations annually which are designed and developed within 293 research projects in different research fields.