Potato Virus Y (PVY) is one of the most important pathogenic agents that reduce the yield and quality of tobacco (Nicotiana tabacum L.). DNA-based molecular markers are valuable tools for identifying germplasm in gene banks, assessing kinship ties, and doing marker-assisted selection (MAS) for resistance to pests, diseases, and some crop traits of interest. This work presents the results of association analysis for resistance to PVY with SSR markers. A total number of 66 alleles were detected using 26 SSR primer pairs on 90 oriental-type tobacco genotypes with an average of 2.54 alleles per locus. A model-based Bayesian approach was used to subdivide 90 tobacco genotypes into three subgroups. Approximately 5.85% of the 325 SSR locus pairs showed a significant level of linkage disequilibrium (LD) (P<0.01). By using GLM procedure, 3 loci (PT30260, PT30046 and PT30061) from linkage groups 8a, 6, and 11 of the tobacco reference map were identified to associate with resistance to PVY in a 10% probability level (P ≤ 0.0615, 0.0839, and 0.072, respectively). SSR locus PT30260 (P≤ 0.077) was also detected with the mixed linear model (MLM) accounting for population structure and kinship relatedness (Q+K model). Linked-resistant SSR markers can be used as indicators of PVY resistance and interest in marker-assisted selection (MAS) in tobacco breeding programs.