The jetliner – owned by Spanish company Swiftair and leased by Algeria's flagship carrier – had 110 passengers and six crew members on board when it took off from Ouagadougou, Burkina Faso, en route to Algiers, the airline said.
Air navigation services lost track of the plane, an MD-83 model, about 50 minutes after it took off.
Two French planes along with Algerian and U.N. forces searched for the plane, said French Foreign Minister Laurent Fabius.
The wreckage was discovered in Mali’s Gossi region near the border of neighboring Burkina Faso, according to a statement from the office of the French president.
The aircraft "has been clearly identified despite its disintegrated state," read the statement.
Metal debris was found at the crash site, according to a statement released today by Swiftair.
French forces, stationed in Mali to help combat al Qaeda and tribal separatists, are tasked with securing the crash site and gathering information. Much of the region is desert, rugged and remote, with few roads and an average high temperature of 101 degrees Farenheit this time of the year.
The airline said that among the passengers were 51 French nationals along with 24 Burkina Faso nationals, six Lebanese, five Canadians, four Algerians, two Luxemburg nationals, one Swiss, one Nigerian, one Cameroonian and one Malian. The six crew members were Spanish.
News of the plane's disappearance came when Swiftair, the Spanish company that operated the plane, released a statement saying the plane had not arrived at its destination.
Transport Minister Jean Bertin Ouedraogo said the plane sent its last message around 0130 GMT (9:30 p.m. EDT Wednesday), asking Niger air control to change its route because of heavy rains in the area.
John Hansman, MIT professor of aeronautics and astronautics, said sand storms can be especially problematic for flight crews.
“Sand storms are really bad because the sand is ingested in the engines, and it can create a problem,” Hansman said.
The flight path of Flight AH5017 from Ouagadougou, the capital of the west African nation of Burkina Faso, to Algiers was not immediately clear.
Ouagadougou is in a nearly straight line south of Algiers, passing over Mali. Northern Mali has been the scene of firefights between the alliance of al Qaeda affiliated fighters and Tuareg separatists against French troops supporting the Mali government.
The crash of the Air Algerie plane is the latest in a series of aviation disasters.
In March, Malaysia Airlines Flight 370 disappeared over the southern Indian Ocean with 239 people on board. No wreckage from the plane has been found.
Last week, a Malaysia Airlines jetliner was shot down over a war-torn section of Ukraine, with U.S. officials blaming it on separatists firing a surface-to-air missile.
On Wednesday, a Taiwanese plane crashed during a storm, killing 48 people.
While fliers are jittery about the tragedies, air travel remains relatively safe. There have been two deaths for every 100 million passengers on commercial flights in the last decade, excluding acts of terrorism. Travelers are much more likely to die driving to the airport than stepping on a plane. There are more than 30,000 motor-vehicle deaths in the U.S. each year, a mortality rate eight times greater than that in planes.
Jetliners such as the one that crashed in Taiwan and Mali are designed to survive storms – but pilots are supposed to fly around bad weather, Hansman said.
“Weather in and of itself shouldn't have been a problem in either of these accidents, but it’s likely to be a combination of the weather and the pilots not being able to react to the weather,” Hansman said.