In Vietnam, cassava mosaic disease (CMD) caused by the Sri Lanka Cassava Mosaic Virus (SLCMV) has been largely controlled in recent years; however, it continues to affect significant areas. To expedite the selection of lines harboring resistance genes against this disease, three Single Nucleotide Polymorphism (SNP) markers were used to screen a population of hybrid cassava lines. Under the natural conditions of Tay Ninh Province, an increasing trend in the severity of CMD was observed within the experimental population. Among the three SNP markers evaluated, S12_7926132 exhibited the highest accuracy at 76.7%, while S12_7926163 demonstrated a comparable accuracy of 76.2%. In contrast, the S14_4626854 marker showed the lowest accuracy, at only 63.5%. Notably, the combination of the S12_7926163 and S14_4626854 markers achieved a maximum accuracy of 80.9% for this population.