Since ex-army chief and now President Abdel Fattah al-Sisi deposed Morsi in July 2013, his followers have been the target of a relentless crackdown by the authorities, who are also accused of exploiting the judiciary in their fight against them.
In October, Sisi issued a decree allowing military trials for civilians suspected of attacking state infrastructure, after a wave of deadly strikes on soldiers.
The 312 Islamists are the latest to face a military trial since the presidential decree widening the jurisdiction of army tribunals was issued.
Violent clashes erupted across the country after the ouster of Morsi, and after the deadly August 14, 2013 dispersal of two protest camps set up by his supporters in Cairo.
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The crackdown since then has left at least 1,400 people dead, and more than 15,000 imprisoned.
Dozens have also been sentenced to death after mass trials which the United Nations says is "unprecedented" in recent history.