The charges, which include arranging fraudulent academic credit, impermissible financial aid and obstructing the governing body's investigation, were outlined in a notice of allegations released by the university on Friday.
There were seven alleged Level I violations -- which are judged the most serious by the NCAA -- in the 43-page notice.
Though things could be worse for the Golden Eagles.
The NCAA notably did not include the dreaded lack of institutional control charge, instead placing most of the blame on Tyndall and his staff during their two-year tenure.
Tyndall went 56-17 at Southern Miss, advancing to the quarterfinals of the National Invitation Tournament in both seasons. The school has 90 days to respond to the NCAA's notice.
Southern Miss released a response to the notice on Friday saying it "understands the serious nature of the allegations" and would continue to work with the NCAA.
The school notes that none of the violations involve current employees and the investigation was limited to the men's basketball program.
"Importantly, the notice does not include a charge of a lack of institutional control or failure to monitor the program by the University," the university said in the statement. "Further, the academic misconduct identified in the notice relates to coursework undertaken at other institutions prior to the students' enrollment at USM."
Tyndall said in a statement he was "very disappointed and saddened at the allegations of NCAA violations." He also said he "did not knowingly violate NCAA rules, nor did I encourage or condone rules violations by anyone on the coaching staff" and that he cooperated with the NCAA's review.
He apologized to the "Southern Miss community for any harm caused by violations that occurred."
Tyndall left Southern Miss to coach atTennesseein 2014.
His stint with the Volunteers was short-lived.
Southern Miss revealed it was under investigation in November, about a week before Tyndall's first game with the Volunteers. Tyndall went 16-16 in his lone season at Tennessee before being fired March 27 for reasons related to the NCAA's investigation.
The allegations levied by the NCAA against Southern Miss and Tyndall were meticulously detailed in the notice. They included:
Basketball staff members completed junior college coursework for seven prospective players, including five who eventually enrolled at the university.
Tyndall provided a player about $6,000 in cash and prepaid cards and another player about $2,000 to help pay for living expenses associated with the school's tuition and room and board.
Tyndall deleted emails pertinent to the NCAA's investigation and contacted individuals in an effort to get them to give the governing body false information.
The NCAA's allegations, which were sent to the school on Wednesday, were largely expected.
In Tennessee's termination letter to Tyndall in March, athletic director Dave Hart said "it's highly likely" that the NCAA will find "Level I and/or Level II violations relating to academic misconduct and impermissible financial aid" occurred while Tyndall was at Southern Miss.
Also in the termination letter, Hart said Tyndall acknowledged deleting emails from an "account maintained at a prior institution." Hart's letter said those deleted emails "could have been relevant to the NCAA's investigation of Southern Miss and/or compliance with NCAA rules."
Tyndall's contract at Tennessee was through March 2020 and would have paid him $1.6 million annually, but Hart said the day he fired him that the terms should prevent the school from owing him any more money.
When he was fired at Tennessee, Tyndall issued a statement through his lawyer in which the coach said he was "surprised and disappointed" after learning violations of NCAA rules occurred when he was coaching Southern Mississippi.
Tennessee athletic department spokesman Jason Yellin said regarding's Friday announcement that "it would be inappropriate for us to comment on the affairs of another institution."
The 45-year-old Tyndall has had previous problems with the NCAA.
When Tyndall was coaching Morehead State in 2010, the program was placed on two years' probation for recruiting violations related to booster activity. The school's self-imposed penalties included the loss of one scholarship and other recruiting restrictions.
Tyndall, Southern Miss hit with Level I violations
ESPN college basketball reporter Eamonn Brennan discusses the seven Level I violations the NCAA has handed down to Southern Miss and former coach Donnie Tyndall.