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The origin of cetaceans (whales, dolphins, and porpoises) has become a popular case study in mammalian evolution. This dissertation utilizes a variety of methods to address the evolution and development of cetacean appendages. Comparative anatomical methods are used to investigate locomotor abilities of a fossil relative to cetaceans. Long bone cross-sectional areas were quantified and modern comparative phylogenetic methods were used to reconstruct character evolution in the limbs of cetaceans and artiodactyls. Experimental molecular techniques are also utilized to answer questions regarding the development of the dolphin forelimb. Fossil findings near the Jammu-Kashmir region along the India-Pakistan border show that a fossil artiodactyl family, Raoellidae, is closely related to cetaceans, lived in an aquatic environment, and never lost its ability to bear weight on land. Using comparative anatomical methods, the postcranial skeleton of the middle Eocene raoellid Indohyus was found to be a digitigrade, cursorial artiodactyl. Indohyus also had a thickened skeleton that may have afforded it a greater ability to swim compared to terrestrial artiodactyls. Vertebrates that occupy an aquatic environment (e.g., Hippopotamus, penguins) have an increased long bone cortical thickness compared to taxa that occupy a terrestrial niche. Little is known of cortical bone evolution in artiodactyls and cetaceans. This study reconstructed cortical bone evolution based on quantitative measures of cortical bone thickness of artiodactyls and cetaceans. Thickened bone evolved only once in artiodactyls, in the common ancestor of fossil anthracotheres, fossil raoellids, cetaceans and hippopotamids. Thickened bone cortices probably acted as skeletal ballast that allowed for the successful invasion of the marine environment. Most mammals have a generalized phalangeal formula with two phalanges in the thumb and three in the remaining digits. Cetaceans are the only mammals that have more than three phalanges per digit (hyperphalangy). Developmental mechanisms generating hyperphalangy are unknown. This study tests the hypothesis that dolphins exhibit greater duration of expression of the genes controlling development of limb growth from the body wall, and joint formation. Studies of protein signals during dolphin ontogeny indicate that the Fibroblast Growth Factors (Fgfs) are active while the forelimb is projecting from the body wall until 30 days gestation, experiences a brief hiatus, and Fgf-8 expression is recapitulated later in development after approximately six phalanges are formed. This recapitulation of Fgf-8 is unlike the generalized mammalian pattern, suggesting that heterochronic changes of expression took place. Cetaceans evolved a flipper consisting of soft tissue encasing bony digits that functions as a hydrofoil. While most mammals develop separated digits, cetaceans retain interdigital tissues during development. The genetic mechanisms that allow for the retention of interdigital tissues in cetaceans are unknown. This study found that a key activator of interdigital cell death, bone morphogenic proteins (Bmps) was active in the developing dolphin limbs, but action of Bmp was inhibited by overlapping signals of two Bmp-antagonists, Gremlin and Fibroblast Growth Factors (Fgfs). Gremlin directly inhibits the apoptotic effects of Bmp, while Fgfs promote the survival and proliferation of interdigital tissues.