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Current analytical characterization of phytochemical is expensive and laborious. Alternatively, techniques such as biosensor with high binding affinity and specificity to the target such as aptamer emerged recently. Aptamers are oligonucleotides with structured molecules that can bind to their targets by specific 3-D conformation. Though aptamer technology have taken place for the past 30 years, little works have been conducted on its capacity to bind phytochemical compounds. Here, DNA aptamers named APT1 to APT30 3-D structures and possible binding mechanism of the aptamers-quercetin complex were evaluated in-silico. Secondary and tertiary structure of 28 potential DNA aptamers candidates were modelled adopting MFold and RNA Composer, respectively. The correspond sequence further modified from RNA to DNA by Discovery Studio Visualizer software. Applying AutoDock Vina, the aptamer-quercetin interactions were predicted. Amongst the aptamers, APT14, APT15 and APT1 displayed highest binding affinity with -9.4, -9.3 and -9.3 kcal/mol, respectively. Upon structure analysis, most of the binding sites that possess high docking energy were positioned at loops and stem conformation. The later plays an important role in stabilization while the bases within the loop motifs responsible in supporting the binding. The stability of potential aptamers-quercetin complex will be further explored for their specific intermolecular interaction using molecular dynamics simulation.