The islets expose serpentinized abyssal mantle peridotite and kaersutite-bearing ultramafic mylonite atop the world's highest and yet only second largest megamullion (after the Parece Vela megamullion under Okinotorishima in the Pacific Ocean). This grouping is the sole location in the Atlantic Ocean where the abyssal mantle is exposed above sea level.
In 1986, the archipelago was designated an environmentally protected area. This is now part of the Fernando de Noronha Environmental Protection Area. Since 1998, the Brazilian Navy has maintained a permanently manned research facility on the islands. The main economic activity around the islets is tuna fishing.
On April 20, 1511, a Portuguese Navy fleet composed of six caravels under the command of Captain Garcia de Noronha discovered the islets by accident while on their journey to India. While navigating in open sea at late night, the Saint Peter caravel, under the command of Captain Manuel de Castro Alcoforado, crashed against the islets. The crew was rescued by the Saint Paul caravel, forming the name given to the islets.
On the morning of February 16, 1832, the rocks were visited by Charles Darwin on the first leg of his voyage on HMS Beagle around the world. Darwin listed all the fauna he could find; noting that not a single plant or even a lichen could be found on the island. Darwin found two birds, a booby and a noddy, a large crab that stole the fish intended for baby birds, a fly that lived on the booby and a parasitic tick. He found a moth that lived on feathers, a beetle, a woodlouse that lived on dung, and numerous spiders that he thought lived on scavengers of the waterfowl. Darwin felt that these rocks represented how life first took hold on a newly formed outcrop. Darwin was correct in noting that, unusually, these small islands were not volcanic, but were instead formed by a geologic uplift. Darwin's account formed the basis of a fictionalized episode in Patrick O'Brian's historical novel HMS Surprise, when the naturalist Stephen Maturin is briefly marooned and survives by drinking fouled rainwater and the blood of boobies.
The then called “St. Paul's Rocks” were visited by James Clark Ross on 29 November 1839. He was in charge of an expedition to the Antarctic regions with two vessels, HMS Erebus and HMS Terror. Robert McCormick gave some geological and biological remarks on St. Paul's Rocks in the report on the expedition.