Known as Marcos, the Zapatista leader and spokesman, wearing a ski-mask, was present at the celebration held in the Zapatistas' base of Oventic, about 735km southeast of Mexico City.
Participants saluted the Mexican and Zapatista flags, and held a large dance and ate traditional tamales and coffee.
The Zapatistas seized the main city of San Cristobal de las Casas and other Chiapas communities in the name of socialism and Indian rights on January 1, 1994.
A ceasefire ended fighting between rebels and government forces after a few days, and the two sides have since maintained an uneasy truce.
Marcos, who has been identified by the government as a professor-turned-guerrilla, has continued to champion a quieter social revolution from the jungles of Chiapas, issuing missives critical of Mexico's politicians and government policies.
Speaking in the Indian language of Tzotzil, Marcos recalled on Sunday night how the movement was founded with the intention of ending the isolation and misery of the Indians.
The Zapatistas have since formed autonomous governments in at least 38 villages in the highlands of Chiapas, as well as "good government committees" that promote their development.
It was the first time in many years that Marcos attended anniversary celebrations. He was escorted by several members of the Zapatista National Liberation Army.