Two dozen people were killed in Gonaïves in 1994 in an army massacre of supporters of Jean-Bertrand Aristide. Later, Gonaïves was the scene of substantial rioting and violence primarily motivated by opposition to Aristide, and on February 5, 2004, a group calling itself the Revolutionary Artibonite Resistance Front seized control of the city, starting the 2004 Haiti rebellion.
In September 2004, Hurricane Jeanne caused major flooding and mudslides in the city. 1,650 people are confirmed dead in Haiti, and the death toll in Gonaïves is expected to top 2,000. Every building in the city was damaged by the storm, and 250,000 people were left homeless.