Fusarium ear rot is considered as one of the major diseases leading to significant yield loss in maize in Vietnam and all over the world. Breeding maize varieties for resistance to ear rot caused by Fusarium with the traditional procedures is not really effective because of very time-consuming and great efforts in transferring resistant genes into promising hybrids. Therefore, applying molecular markers in breeding and developing maize varieties resistant to Fusarium would be more feasible. Up to now, through the pplication of SSR markers and evaluation of resistance among maize germplasm, 6 simple sequence repeat (SSR) markers (Umc1025, Dupssr34, Nc030, SSR93, Umc1489, andUmc1511) linked to Fusarium ear rot genes in maize plants have been identified. In this study, 6 SSR markers were used in F5 and BC5 maize populations to select promising inbred lines resistant to Fusarium ear rot. The result showed that 11 lines with SSR markers responsible for resistance to Fusarium ear rot were found, including 3 lines with 1 marker, 5 lines with 3 markers, and 2 lines with 4 markers. 8 lines (F5.5, F5.12, F5.18, F5.22, BC5.8, BC5.9, BC5.21, and BC5.22) with at least 2 markers were selected for a maize breeding program; hybrid combinations THL5, THL25, THL6 and THL12 of at least 3 markers linked with the resistance to Fusarium ear rot were selected for further development in production.