Recent upgrading of the Facility for Modification and Analysis of Materials with Ion Beams (FAMA), in the Laboratory of Physics of the Vinča Institute of Nuclear Sciences, included modernization of its electron cyclotron resonance (ECR) ion source. The ECR ion source was extensively used for production of multiply charged ions from gases and solid substances for more than 15 years, during which time its major subsystems were expended and therefore, it required complete reconstruction. As a part of this reconstruction we designed and put together a completely new control system of the ECR ion source. It is a distributed and fiber-optically linked control system based on the Group3 Control hardware and the control application written in the Wonderware’s In Touch software. The control system should help and assist an operator in obtaining the appropriate operating parameters of the ECR ion source, maintaining and controlling operating parameters of the machine during its operation, as well as in monitoring weather the safety conditions are fulfilled during the operation of the machine. We tested the operation and performances of the new control system during the commissioning of the upgraded ECR ion source. Compared to the old one, the new system is more reliable, more userfriendly oriented, and it comprises several new useful control applications. [Projekat Ministarstva nauke Republike Srbije, br. III 45006]