Fine-grained recognition refers to a subordinate level of recognition, such are recognizing different species of birds, animals or plants. It differs from recognition of basic categories, such as humans, tables, and computers, in that there are global similarities in shape or structure shared within a category, and the differences are in the details of the object parts. We suggest that the key to identifying the fine-grained differences lies in finding the right alignment of image regions that contain the same object parts. We propose a template model for the purpose, which captures common shape patterns of object parts, as well as the co-occurence relation of the shape patterns. Once the image regions are aligned, extracted features are used for classification. Learning of the template model is efficient, and the recognition results we achieve significantly outperform the state-of-the-art algorithms.