The Presidio is rich in archaeological resources, spanning from Native American sites dating back more than 1200 years, through the Spanish and Mexican periods from 1776 to 1846, and ranging through the U.S. occupation. Three main archeological project areas have been studied in recent years.

A major archaeological recovery project was carried out by the National Park Service at Crissy Field in conjunction with the Crissy Field Restoration Project. Although the field portion of the recovery project is over, the vast number of artifacts recovered are still being cataloged and studied.

Spanish Chapel

The chapel area of the original Spanish presidio was excavated by Cabrillo College classes over a number of summers. This work found a number of Spanish artifacts and defined the "footprint" of the Spanish chapel, allowing better determination of the exact placement of the Spanish Presidio structure.

Funston Avenue

The University of California, Berkeley, has conducted research along Funston Avenue in order to identify and investigate archaeological sites from the Spanish through early U.S. periods. This information will be used to understand, preserve and educate visitors about the sensitive archaeological resources in the heart of the Presidio.