Most of the approaches which address the problem of 3D object retrieval, use global descriptors of the objects which fail to consistently compensate for the intra-class variability of articulated objects. In this paper, a retrieval methodology is presented which is based upon a graph-based object representation. This is composed of a meaningful new mesh segmentation along with a graph matching between the graph of the query object and each of the graphs that correspond to the objects of the 3D object database. The graph matching algorithm is based on the Earth Mover's Distance (EMD) similarity measure which is calculated using a new ground distance assignment. The superior performance of the proposed methodology is shown after an extensive experimentation comprising alternative descriptors for the constituent components of the 3D object as well as comparison with state of the art retrieval algorithms. Categories and Subject Descriptors (according to ACM CCS): Pattern Recognition ...