A near-infrared (near-IR) fluorescence quenching method was developed for the determination of nucleic acids in aqueous solution by using a cationic heptamethylene thiacyanine as a probe. The near-IR cationic cyanine showed maximum excitation and emission wavelengths at 800 and 825 nm, respectively, in the presence of Triton X-100; the fluorescence of the cyanine could be greatly quenched by DNA. The calibration graphs were linear over the range of 10-400 ng/mL for CT (calf thymus) DNA and over the range 5-400 ng/mL for FS (fish sperm) DNA under optimal conditions. The corresponding detection limits were 5.2 ng/mL for CT DNA and 2.5 ng/mL for FS DNA. The relative standard deviation (n = 8) was 3.1% for 75 ng/mL CT DNA and 2.2% for 75 ng/mL FS DNA, respectively. Preliminary research showed that the fluorescence quenching might be ascribed to the formation of dye aggregate facilitated by DNA.