Evaluating stress and strain fields in anatomical structures is a way to test hypotheses that relate specific features of facial and skeletal morphology to mechanical loading. Engineering techniques such as finite element analysis are now commonly used to calculate stress and strain fields, but if we are to fully accept these methods we must be confident that the applied loading regimens are reasonable. Multibody dynamics analysis (MDA) is a relatively new three dimensional computer modeling technique that can be used to apply varying muscle forces to predict joint and bite forces during static and dynamic motions. The method ensures that equilibrium of the structure is maintained at all times, even for complex statically indeterminate problems, eliminating nonphysiological constraint conditions often seen with other approaches. This study describes the novel use of MDA to investigate the influence of different muscle representations on a macaque skull model (Macaca fascicularis), where muscle groups were represented by either a single, multiple, or wrapped muscle fibers. The impact of varying muscle representation on stress fields was assessed through additional finite element simulations. The MDA models highlighted that muscle forces varied with gape and that forces within individual muscle groups also varied; for example, the anterior strands of the superficial masseter were loaded to a greater extent than the posterior strands. The direction of the muscle force was altered when temporalis muscle wrapping was modeled, and was coupled with compressive contact forces applied to the frontal, parietal and temporal bones of the cranium during biting.