Indigenous was a term that meant that something was native to or naturally occurring in a place. The word also applied to groups of people that were native to a particular place.
People[]
The North, Central, and South American regions of Earth were home to a number of indigenous Human ethnic groups. (TAS: "How Sharper Than a Serpent's Tooth") Those areas were heavily colonized by more technologically advanced Humans from other continents after the 15th century, leading to the destruction of many of these indigenous cultures. (TNG: "Journey's End")
In 2268, Kirk and the USS Enterprise encountered a number of indigenous peoples from Earth, including people from the Delaware, Navajo, and Mohican tribes, on a planet where they had been transported by the Preservers several centuries earlier, so that they could live undisturbed. (TOS: "The Paradise Syndrome")
General terminology[]
In July 2151, Enterprise encountered a humanoid species on their homeworld homeworld. While scanning the planet, Archer asked T'Pol to scan for non-indigenous biosigns. While there, the Enterprise crew discovered that Garos, a newcomer to the planet, claimed that a mysterious disease affecting the locals was indigenous, when it was actually caused by Garos' antimatter reactor. (ENT: "Civilization")