The Deep Ones are a race of ocean dwelling beings. They are functionally immortal and fish-frog-human like creatures. They follow and worship their monarchs and gods, Father Dagon and Mother Hydra, though they revere Great Cthulhu as their primordial deity.
Strangely, the origins of the Deep Ones are still unclear. One theory is that they probably followed Dagon, Hydra and Cthulhu to Earth from outer space. Following the defeat of Cthulhu and the sinking of R'lyeh, they were left alone.
Much of their history is unknown until Obed Marsh, a ship captain from Innsmouth, met them in the Polynesian islands in the Pacific Ocean. After this, Obed contacted one of their cities along the coast near Innsmouth : Y'ha-nthlei. Seeking to bring his town back from decline, Marsh soon entered into a pact with them and offered human sacrifices in exchange for fish and gold. An interesting thing to note is that the Deep Ones actually built Y'ha-nthlei on the ruins of a Flying Polyps' prison.
When Marsh was arrested in 1846, the Deep Ones came to aid their ally, killing half of the town's citizens that day. Those who survived were forced to take the Oaths of Dagon, the third one including interbreed with the Deep Ones, creating the human-Deep One hybrids that would one day evolve and live forever in Y'ha-nthlei.
The Deep Ones are described as being pretty much everywhere around the seas of the world, waiting for the rise of Cthulhu to take place by his side. It is unknown, though likely, if the ones in Innsmouth survived the U. S. torpedo attack of 1922 when Y'ha-nthlei was destroyed.