Penguins breathe with their lungs. Birds like penguins have no skin and gills in their respiratory system, so they breathe with their lungs. Only amphibians breathe through the skin and gills. Penguins don't breathe in water. It breathes when it goes ashore and doesn't breathe when it dives. Penguins are typical seabirds. Although he can't fly, he is a super swimmer among birds.