​İzmir Agricultural Quarantine Directorate was established in Plant Protection Research Institute Bornova under the name of  Quarantine Chieftainship, in 1 March  1950. 

Once Law on Plant Protection and Agricultural Quarantine, No 6968, came into force in 15 May 1957, it was renamed as  Agricultural Quarantine and Fumigation Directorate subject to  Ministry of Food, Agriculture and Livestock. 

The name of directorate has been renamed  as Regional Agricultural Quarantine Directorate because of its extended working area from Bandırma to Fethiye in 1 March 1966. In 1968, circulating capital was established to conduct activities well. 

Reorganization and reconstruction of the Ministry of Agriculture, Forestry and Rural Affairs in 1985 led to the directorate to participate in Directorate of Provincial Food, Agriculture and Livestock. Since  1990, the directorate  has been conducting its activities in Alsancak. 

It was acted by depending upon the Ministry of Agriculture and Rural Affairs  between the years of  1996-2000. In 2000-2008, it was subject to  Directorate of Provincial Food Agriculture and Livestock and since 2008 it has been carrying activities within the Ministry of Food, Agriculture and Livestock, directly. The laboratory was involved in directorate ever since 2005 and there has been no modification on activities and its name within the  law of establishment on Ministry of Food, Agriculture and Livestock.