Provided is a heterogeneous DNA barcoding method which includes the steps of: (a) providing a DNA microarray comprising DNA spots which can be distinguished from each other by a barcode base sequence; (b) providing a microwell array which is equipped with microwells that correspond to the spatial arrangement of the DNA spots on the DNA microarray; (c) loading a sample solution containing the target base sequences to the microwells; (d) combining the DNA microarray with the microwell array and forming fine reaction spaces by spatially separating the DNA spots by the microwells; (e) allowing the base sequence of the DNA spot to undergo reaction with the target base sequence of the sample, in the fine reaction space, and combining the information on the base sequence of the DNA spot with the information on the base sequence of the sample; and (f) separating the DNA microarray from the microwell array and obtaining the resulting product comprising the barcode base sequence.
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