This study focused on the implementation of microsatellite markers to determine the diversity among elite inbred lines representing the Vietnamese maize breeding program. Genetic relationships were assessed using twenty loci to gain an understanding of the width of the program compared to other Asia programs, as well as develop a DNA fingerprint database. The PIC value of the 20 loci ranged from 0.10 to 0.83 with those containing a tetra-repeat the most informative (mean PIC = 0.60). The amount of genetic diversity among the lines assessed was similar to the levels identified in other Asian breeding programs. Future monitoring will be important to maintain genetic breadth of the Vietnamese program and minimize risks from narrowing in future targeted selective breeding strategies. This will be facilitated through implementation of the developed robust SSR-based DNA fingerprint database, which will also be used for true-to-type identification, hybrid confirmation and potential trait selection.