Optical coherence tomography (OCT) is a recent imaging method that allows high-resolution, cross-sectional imaging through tissues and materials. Over the past 18 years, OCT has been successfully used in disease diagnosis, biomedical research, material evaluation, and many other domains. As OCT is a recent imaging method, until now surgeons have limited experience using it. In addition, the number of images obtained from the imaging device is too large, so we need an automated method to analyze them. We propose a novel method for automated classification of OCT images based on local features and earth mover's distance (EMD). We evaluated our algorithm using an OCT image set which contains two kinds of skin images, normal skin and nevus flammeus. Experimental results demonstrate the effectiveness of our method, which achieved classification accuracy of 0.97 for an EMD+KNN scheme and 0.99 for an EMD+SVM (support vector machine) scheme, much higher than the previous method. Our approach is especially suitable for nonhomogeneous images and could be applied to a wide range of OCT images.