Atlantis was a subaquatic city and capital of the Atlantean Empire.
Atlantis was a Atlan city before it was sunk in the great cataclysm created by the Atlan Empire against Apocalypse. The city was soon settled by the water-breathing Homo mermanus led by the current king Namor.
Atlantis is the name of the actual mythological place in real time and in both fictional universes of DC Comics and Marvel, but the civilizations from these universes are different by biology. The Marvel Atlanteans have evolved into more aquatic species whereas their counterparts in the DC universe retain their human appearance but also breath underwater.