The African Seed Trade Association arose out of a need to have a regional representative body for the seed industry, which could also serve to promote the development of private seed enterprises.

A range of African and international stakeholders commenced discussions early in 1997. This developed into a preparatory meeting held in Malawi in April 1999 where an Ad Hoc working group was nominated.
The group developed a draft constitution, by laws, and budgets, which were finalized at a meeting in Kenya in August 1999. AFSTA was formally established on March 20 - 21, 2000, during an inaugural congress in South Africa. Kenya was elected as host country for the Secretariat.