San Pedro Martir is also unique in the area for its year-round quantity of birds. The island is the only island in the area with a perpetually swirling cloud of sea birds. The large bird population deposits enormous quantities of guano on the island, resulting white appearance of the island with sparse vegetation. The blue-footed booby is common on the island, using the island as nesting grounds. Sea lion rockeries also ring the island.
The Seri Indians created benches to attract nest building and ease of egg collection, the sole evidence of human intervention visible on the island. In the late 19th and early 20th century guano was heavily mined off the island and shipped as far as Europe for use as fertilizer. Mining boats brought the black rat as an invasive species to the island. The rats were eradicated in the fall of 2007 by spraying rat poison on the island.
San Pedro Martir is seldom visited, having near vertical sides leaving only questionable fair weather anchorages in two locations. Landing access was possible near a small isthmus in the southeast of the island, but is now forbidden. In 2005, the island was classified along with 244 others as a World Heritage Site by UNESCO, and included in the Islands and Protected Areas of the Gulf of California.