The Florida Museum Historical Archaeology collections consists of more than 2 million excavated specimens from more than 100 sites throughout Florida and Latin America.

They include the largest known systematic collection of Spanish colonial archaeological specimens in the country, representing sites of domestic, military, religious and commercial sites dating from 1492 through the nineteenth century. The collection also incorporates archaeological specimens from a variety of non-Spanish eighteenth and nineteenth century sites, including homesteads, plantations, trading posts, forts and towns.

In addition to systematic collections resulting form excavation, the program also maintains extensive collections of type specimens, comparative specimens and published specimens for historical archaeology (ceramics, beads, weaponry, architectural items, pipes, buttons, glassware, etc.). These include type collections developed by John Goggin, Charles Fairbanks, José Cruxent, Florence and Robert Lister and Kathleen Deagan. The materials span the period of 1493-1900, and are used extensively as a reference collection, a comparative collection and a teaching collection.