The college was established in 1956 as the Southern Mindanao branch of the Philippine Institute of Fisheries Technology (PIFT), the predecessor of the U.P.

From 1995 to 2003 the ZSCMST served as the center/lead agency of the Southern Mindanao Aquatic Resources Research and Development Zonal Network.

It has served as a zonal center for fisheries and marine biodiversity of the Mindanao Advanced Education Project of the CHED.

It is a 10 Kilowatts FM broadcast station serving the city of Zamboanga and nearby province of Basilan.

In December 2023, Marino News FM shut down its terrestrial operations temporarily due to upgrading of equipment and maintenance activities.