Growing interest in the development of bio-inspired autonomous underwater vehicles (AUVs) has motivated research in understanding the mechanisms behind the propulsion systems of marine animals. For example, the locomotive behavior of rays (Batoidea) by movement of the pectoral fins is of particular interest due to their superior performance characteristics over contemporary AUV propulsion systems. To better understand the mechanics of pectoral fin propulsion, this paper introduces a biomechanical model that simulates how batoid skeletal structures function to achieve the swimming locomotion observed in nature. Two rays were studied, Dasyatis sabina (Atlantic ray), and Rhinoptera bonasus (cownose ray). These species were selected because they exhibit very different swimming styles (undulation versus oscillation), but all use primarily their pectoral fins for propulsion (unlike electric rays or guitarfishes). Computerized tomography scans of each species were taken to image the underlying structure, which reveal a complex system of cartilaginous joints and linkages. Data collected from these images were used to quantify the complete skeletal morphometry of each batoid fin. Morphological differences were identified in the internal cartilage arrangement between each species including variations in the orientation of the skeletal elements, or radials, and the joint patterns between them, called the inter-radial joint pattern. These data were used as the primary input into the biomechanical model to couple a given ray skeletal structure with various swimming motions. A key output of the model is an estimation of the uniaxial strain that develops in the skeletal connective tissue in order for the structure to achieve motions observed during swimming. Tensile load tests of this connective tissue were conducted to further investigate the implications of the material strain predictions. The model also demonstrates that changes in the skeletal architecture (e.g., joint positioning) will effect fin deformation characteristics. Ultimately, the results of this study can be used to guide the design of optimally performing bio-inspired AUVs.