After the first rains of winter, Farallon weed sprouts appear on the rocky landscape and by February a lush carpet of green plants and yellow flowers covers most of the island. Seaside daisies and their purple flowers fill crevices on shear rock walls while low growing Spurgelaria covers large patches of the marine terrace. Invasive species are interspersed on the southern side of Southeast Farallon Island; New Zealand spinach and malva have been the targets of intensive control efforts for years, while other invasives such as plaintain and annual grasses are controlled opportunistically. These non-native species grow during the seabird breeding season and cover up important nesting areas.Dozens of eucalyptus and other trees were planted by early residents before Southeast Farallon Island became part of the refuge but the unyielding wind and shallow, gravelly soil foiled all attempts to create a "Farallon forest." Four cypress trees and one Monterey pine, growing on the leeward side of the buildings are all that remain of these trees.
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Farallon National Wildlife Refuge is managed as part of the San Francisco Bay National Wildlife Refuge Complex.