The dead were killed and buried in shallow pits or dumped in grasslands just near the national highway in Maguindanao province.
Ampatuan Jr is accused of leading the killings to prevent Mangudadatu from challenging him in the May 2010 race to succeed his father, Andal Ampatuan Sr, as provincial governor.
Ampatuan Sr as well as several other clan members were later arrested after martial law was imposed in Maguindanao and charged separately with rebellion.
In a report to Philippine congress defending the imposition of martial law in the wake of the killings, Gloria Arroyo, the Philippine president, said those massacred bore "marks of despicable torture, contempt and outrageous torment".
She also said that clan followers had threatened to carry out attacks if their patrons were arrested.
However the Brussels-based International Crisis Group said last month that Arroyo was partly to blame for the massacre because she had allowed a "local despot to indulge his greed and ambition".
Ampatuan Sr had controlled Maguindanao province for most of the past decade and was grooming his son to take his place as governor in national elections scheduled for May.
Ampatuan Sr's influence and power grew because Arroyo allowed him to maintain a 3,000-strong heavily armed militia as part of a government strategy to contain Muslim separatist insurgents in the south.
In exchange for that support, Ampatuan also helped deliver votes from the province to Arroyo and her allies in the 2004 election.
The shocking crime forced her to cut political ties with the clan, but critics say the Ampatuans may still hold enough political power to avoid severe penalties.