There are five families of reptiles on the islands: iguanas, lava lizards, geckos, snakes and the giant tortoises. The Galápagos and the Seychelles are the only two island groups in the world which are inhabited by giant tortoises. Of the 27 species of reptiles on the islands, 17 are endemic.

Half of the resident population of birds is endemic to the Galápagos, but only 5 of the 19 species of sea birds found on the Galápagos are unique to the islands. These are: the Galápagos penguin, the flightless cormorant, the lava gull, the swallowtail gull and the waved albatross. There are 29 species of land birds on the islands, 22 of which are endemic.

The number of native mammals is limited to two species of bats, a few species of rats and, of course, sea lions and seals.

The Galápagos are washed by three currents which provide the islands with a rich and diverse underwater fauna. The number of species of fish has been estimated at 306 , 17% of which are endemic. 16 species of whales and 7 species of dolphins are also in evidence around the islands.