Nigerian separatist militia leader Mujahid Dokubo Asari has been charged with treason for which he could face the death penalty.
Asari says he wants Ijaws to benefit more from Nigeria's oil wealth
Mr Asari denied that charge and several others including unlawful assembly and conspiracy in a court in the capital.
He shouted "Freedom to my people!" before being led from the courtroom.
He was detained two weeks ago following a newspaper interview in which he was quoted as calling for the dissolution of Nigeria.
His arrest sparked protests in the oil-producing Niger Delta region in southern Nigeria.
Mr Asari says he is fighting for the self-determination of the Ijaw people and greater local control of the profits from the oil and gas industries.
The BBC's Mannir Dan Ali in Abuja says that if convicted by the court for treason, Mr Asari could be sentenced to death or face life imprisonment.
It is not clear how his Niger Delta People's Volunteer Force (NDPVF) will react to these charges that carry such steep penalties, our correspondent says.
Hundreds of armed police blocked roads surrounding the Abuja court.
After his detention two weeks ago, Mr Asari's supporters threatened oil production in the Niger Delta if he was not released and at one point US oil company Chevron was forced to shut down one of its facilities in the area.
The NDPVF also told expatriate oil workers to leave the area, but later withdrew the threat.
The Niger Delta remains one of Nigeria's poorest and least developed regions, although it accounts for most of the 2.4 million barrels of oil produced by Nigeria, Africa's largest oil-producer, each year.
Last year, the NDPVF contributed to a sharp rise in world oil prices when it threatened war against oil companies.
Mr Asari will be held in custody until his next appearance in court on 10 November.