Fernandina is considered to have one of the world's most pristine island ecosystems, free from the invasion of foreign species. Undoubtedly one of the most significant inhabitants of Fernandina is the flightless cormorant, an endemic Galapagos species which have formed a colony along the island's coast.  The cormorant evolved into a flightless species on the island, which at the time, was completely free of predators. Their need to fly was unnecessary and subsequently lost. Whilst their ability to fly has disappeared, these cormorant's legs have evolved to be heavier and more powerful and consequently better capable of propelling themselves through the water in the pursuit of fish prey.

Other significant birdlife to be found on Fernandina include the endemic Galapagos penguins, pelicans and Galapagos hawks.  Herons and egrets can often be seen foraging amongst the mangrove roots.