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Complementary DNA microarray technology is a powerful tool in many areas. Usually a two channel microarray red-green (RG) image is obtained. Due to the nature of cDNA microarray technology, a number of impairments affect the cDNA microarray image before the analysis such as identification of differentially expressed genes. Microarray image processing plays a crucial role in the extraction and quantitative analysis of the relative abundance of the DNA product. In this paper, a method combined K-means clustering algorithm and mathematical morphology is presented. Mathematical morphology is a useful tool for extracting image components. K-means clustering algorithm has a good performance in the segmentation of microarray image processing. The result of the experiment shows that the method presented in this paper is accurate, automatic and robust.