Many of the marchers held burning torches and hundreds of motorcyclists brought up the rear.
Saturday's march ended peacefully.
The 1996 incident involved two uninhabited islets off the Turkish coast whose ownership is disputed by Turkey and Greece.
Nationalists from both countries planted flags on the islets, and a military confrontation between the two nations was only averted after U.S. intervention. Three Greek navy officers died when their helicopter crashed during a reconnaissance mission in the area.
Withdrawal of the Greek flag was seen by nationalists as a shameful capitulation.