We present a novel method for the detection of single base mismatch based on fluorescence quenching that unmodified CdS quantum dots exhibit upon aggregation. Target DNA sequences of interest are breast cancer 2 (BRCA2) and signal-induced proliferation-associated gene 1 (Sipa1) sequences. We monitor aggregation of CdS quantum dots upon addition of double-stranded DNAs at different salt concentration using quasi-elastic light scattering (QELS), transmission electron microscopy (TEM), photoluminescence spectroscopy, and zeta potential measurement. Our results indicate that the double-stranded DNA with a perfectly matched sequence can easily be discerned by naked eye from the single base mismatched one due to the fluorescence quenching phenomenon caused by selective aggregation of the CdS quantum dots.