Y'ha-nthlei was the city of the Deep Ones built above the foundations of the prison for the Flying Polyps; near Devil's Reef.
When Obed Marsh, a ship captain from the local town of Innsmouth, summoned the Deep Ones it was the begining of a long lasting alliance between the two races. Since there are evidence that the Kanakies were destroyed by the neighbouring tribes, it is safe to belive, that this act was the trigger for the Deep Ones to settle on Devil's Reef. After the sloughter of 1846 and the forcing of the "Oaths of Dagon", the people of Innsmouth started to mate with the Deep Ones on large scale.
In time, the children of this marriages evolved into Deep One-Human hybrids. As they couldn't live on land any longer, they moved to Y'ha-nthlei. Those who were shun by the people on land, were now free to walk among their Deep One brothers. This all lasted until 1922 when the U. S. Navy led an attack on the city; when it was higly damaged, and most probably abandoned.
The city was made of mostly natural, air filled tunnels. The Temple and the main hall dominated the city. The city had been conected with the town of Innsmouth with tunnels and a portal leading to the old Masonic Temple. The city also had a prison and laboratory. It is known that Esther Marsh, an unknown member of the Marsh familly, had been trying to cultivate new breeds of plant life; inspired by prehestoric plants. It was here that Esther attempted to create bio-chemical weapon, which was later on discovered by the FBI, and which lead to the downfall of the Marshes.