This paper considers ship route extraction and clustering problem based on Automatic Identification System (AIS) data. For the ships with known Maritime Mobile Service Identify (MMSI), we propose a ship route extraction method by using AIS data. For ship route clustering, hierarchical clustering method is selected. We firstly define a distance between ship routes to measure the dissimilarity of them. And then, basic agglomerative clustering algorithm is briefly introduced and some modifications are made on the basic algorithm to make it applicable for ship route clustering problem. The proposed ship route extraction method and modified clustering algorithm are applied to a real case study. Experimental results indicate that the proposed methodology performs well on ship route extraction and clustering problem.