This dissertation presents an archaeology of isolation through the study of a nineteenth century maritime quarantine station in Puerto Rico, using a system that was transplanted from temperate Spain to one of its tropical colonies. Located in Isla de Cabras during the late nineteenth century, this isolation facility was converted into a leper colony and a military camp in the twentieth century. The intensive and continuous use of Isla de Cabras presented the possibility of finding archaeological deposits associated with the quarantine activities as well as post-depositional events. A research model that takes into consideration the specifics of a quarantine station was developed in order to incorporate historical information from archival, cartographic and photographic sources, as well as information from other quarantine sites around the world in order to compare and contrast. The archaeological excavations were geared towards the areas where daily activities had taken place. The analysis of the historical and archaeological information have demonstrated the usefulness of this research approach.