The submarine environment surrounding Malpelo is defined not only by its isolation but also by its location, which is highly influenced by the convergence of several diverse marine currents. This phenomenon creates a focus in the usual dispersion of marine fauna throughout the Indo and Tropical Eastern Pacific.Malpelo is home to an important coral formation as well as a large variety and quantity of marine creatures. Of special interest are hammerhead sharks with awe-inspiring schools of 300 hundred individuals commonly encountered. The two most outstanding phenomena in Malpelo are the huge numbers of free swimming and cluster moray eels along with the colossal congregations of silky sharks that often join with hammerheads to form enormous mixed schools. Extraordinarily, Malpelo is one of the few places that a diver may chance upon the elusive Small Tooth Sand Tiger, which is also known as the Spotted Ragged-tooth shark (Odontaspis ferox).
Other common sights are the white tip shark, Galapagos shark, giant schools of angel fish, Creole fish, jacks, tuna, several ray species including the giant Manta and occasionally a sail fish, whale shark and even Humpback Whale.
The island is visited by some 12 species of migratory birds, including the Red-billed Tropic bird, Red-footed Booby, Black Noddy and the Great or Magnificent Frigate bird (Fregata magnificens). Endemic to the island are one crab species, two sea-stars, various species of coralline fish, and two reptiles.
Algae, moss and lichens cover the rugged cliffs of Malpelo, which host the second largest Masked Booby colony in the world, consisting of approximately 25,000 birds.