The suspects, both Syrians, stand accused of "causing death by deliberate negligence" and "migrant smuggling" after five Syrian refugees including Kurdish toddler Aylan Kurdi died when their boat sank in September while on its way to Greece, state-run Anatolia news agency reported.
The sight of Aylan's body, face down in the sand on a beach outside the southwestern resort of Bodrum, caused an outpouring of anger across the world, pressuring European leaders to begin to tackle the refugee crisis.
His father, who survived, returned to the Syrian town of Kobane to bury his family.
The prosecutors' indictment was sent to the criminal court in Bodrum, Anatolia said, adding that an investigation was underway to identify six other suspects including four Turks.
The report, which did not identify the two suspects, said prosecutors are demanding separate 35-year jail sentences for each of them.
After the indictment's approval by the Bodrum court, a hearing date will be fixed.
Turkey is currently hosting up to 2.5 million Syrians after declaring an open door policy when the conflict in Syria erupted in 2011.
After a key agreement with the European Union last month, Ankara has stepped up efforts to stop migrants from leaving its soil in search of better opportunities in EU member states.
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