In this paper, we propose an image fingerprinting system which uses color histograms of affine covariant regions as a local fingerprint of an image. Given a query, the system first extracts local fingerprints from affine covariant regions. The local fingerprints are based on the color histogram, and the affine covariant regions are detected using the maximally stable extremal region (MSER) detector. After extracting local fingerprints, the system searches local fingerprints in fingerprint database for the nearest neighbor of the query local fingerprints. Then, the query image is identified. Experimental results show that that our system is robust against cropping, resizing, rotation, and small color changes with small computational cost.