Malpelo Island consists of a sheer and barren rock with three high peaks, the highest being Cerro de la Mona with a height of 300 metres (980 ft). It is the only island that rises above the surface from the Malpelo Ridge, which is a solitary volcanic submarine ridge that extends in a northeast-southwest direction with a length of 300 kilometres (190 mi) and a width of 100 kilometres (62 mi). This island is surrounded by a number of offshore rocks. Off the northeast corner are the Tres Mosqueteros. Off the southwest corner are Salomon, Saul, La Gringa, and Escuba. As an oceanic island, this island has never been connected with any other islands or the mainland.
Malpelo Island is composed of Miocene pillow lavas, volcanic breccias, and basaltic dikes that have been dated as being 16 to 17 million years old. This island and the underlying and underwater Malpelo Ridge were created along with the Carnegie Ridge in the Late Miocene by a very complex interaction between the Cocos-Nazca Spreading Centre and the Galápagos hotspot. At first glance, the island seems to be barren rock, devoid of all vegetation. But deposits of bird guano have helped colonies of algae, lichens, mosses and some shrubs and ferns establish, all of which glean nutrients from the guano.
The Malpelo Nature Reserve, a plant and wildlife sanctuary, is defined as a circular area of radius 9.656 kilometres (6.000 mi). On July 12, 2006, Malpelo was declared by UNESCO as a natural World
Heritage Site. A Colombian foundation is trying to preserve the biodiversity of the site. Malpelo is home of a unique shark population; swarms of 500 hammerhead sharks and hundreds of silky sharks are frequently seen by diving expeditions, making it a very popular sharkdiving location.
Malpelo is one of the few places where the Smalltooth sand tiger has been seen alive, in the dive site "El bajo del Monstruo" it is frequently seen. The Dominion of Melchizedek, an unrecognized micronation known for its involvement in large scale fraud, claims sovereignty over it as a "territory". Malpelo counts as a separate "entity" for amateur radio credit. Because of the rugged terrain, strong currents, and remote location the island is rarely activated. A DX-pedition occurred in early 2012, with the operators making 195,292 contacts under very difficult conditions.