Local officials and drug runners are among the 56 people, including 22 police officers, who have been arrested over the disappearance of the students.
Mexico's attorney general said that there is clear evidence that the mayor gave the order to police to target the students to prevent them from interrupting a speech that his wife was giving in the town of Iguala.
Other speculation is that the students were killed for failing to pay extortion money to the a gang.
Two arrested drug gang members led authorities to the site of the mass grave where human remains were found.
The grave was found 10 miles from where the students were last seen.
The students are from a rural teaching college. Last year they took part in a violent occupation of city hall to protest the murder of a local activist.

On the run

The mayor, his wife, and the police chief are now on the run from authorities and there is no seen of the missing 43 students.
Mexico's Attorney General Jesus Murillo Karam said that police officers handed the students over to a drug gang in the Mexican state of Guerrero.
The attorney general has come under enormous nationwide pressure to find those responsible. The city hall of the town of Iguala was burned last week by protesters.
We have the people who carried out the abduction of these individuals.Jesus Murilla Karam, Mexico's attorney general
Protests have also occured in Texas, Venezuela, London and Paris.
"We have the people who carried out the abduction of these individuals," Mr Murillo Karam told reporters.
At the time, eyewitnesses said that the students were bundled into police cars shortly after police shot at buses carrying them, killing six people including three students.
The men arrested for the abduction itself are believed to all be from the group Guerreros Unidos (United Warriors).