Many environmental factors dictate the distribution of vegetation and plant communities at the Presidio. These include climatic factors, such as temperature, exposure to sun and wind, and available moisture; geologic factors, such as bedrock and and soil types. Recently, human factors, such as land disturbance and introduced plants, have altered plant distributions at the Presidio.

Local environmental influences led to a high diversity of plants at the Presidio, and many species have a very limited geographic range (endemic species). As a result, the Presidio today is home to a high density of rare and endangered species, finding refuge in this island surrounded by the City of San Francisco.

The Presidio still preserves tiny remnants of the original San Francisco landscape in its nooks and crannies, and restoration projects are re-introducing native plants to areas where they have long been eradicated. In the spring and early summer, wildflowers abound in many of the natural areas.

Yet, the modern landscape looks very different from that which the Europeans encountered on their arrival in 1776. They introduced non-native plants, grazed livestock, and cut down the few native tree species that grew here.