Color in an image is resolved to 3 or 4 color components and 2-Dimages of these components are stored in separate channels. Most of the color image enhancement algorithms are applied channel-by-channel on each image. But such a system of color image processing is not processing the original color. When a color image is represented as a quaternion image, processing is done in original colors. This paper proposes an implementation of the quaternion approach of enhancement algorithm for enhancing color images and is referred as the modified alpha-rooting by the two-dimensional quaternion discrete Fourier transform (2-D QDFT). Enhancement results of this proposed method are compared with the channel-by-channel image enhancement by the 2-D DFT. Enhancements in color images are quantitatively measured by the color enhancement measure estimation (CEME), which allows for selecting optimum parameters for processing by thegenetic algorithm. Enhancement of color images by the quaternion based method allows for obtaining images which are closer to the genuine representation of the real original color.