Previous studies of the odontocete forelimb have not considered flipper anatomy in an evolutionary context. This study of 39 cetacean species (1 extinct archaeocete, 31 extant and 3 extinct odontocetes, and 4 mysticetes), provides a detailed comparative analysis of the major bones and muscles of the odontocete flipper. Differences across families in the anatomy of the deltoid, supraspinatus, coracobrachialis, and subscapularis muscles correspond directly to size and shape of forelimb elements. Specialization of the different shoulder girdle muscles allows for more maneuverability of the flipper by independent control of muscular columns. Maximum likelihood analyses helped determine the correlation of characters studied by ancestral state reconstruction, and revealed independent evolution of osteological and external characters among various lineages. Comparative Analyses by Independent Contrast (CAIC), found several contrasts between flipper area and body length for several extant odontocetes and a linear relationship was inferred. Degree of hyperphalangy and the soft tissue encasing the flipper helped determine three flipper morphologies based on aspect ratio (AR) and qualitative data. These results suggest that differences in flipper shape have an evolutionary component and are likely largely in response to ecological requirements.