The Muslim man, identified in court documents as Alain N. B, blamed the Christians for rough seas, 29 survivors testified.He forced six men off the boat, sending them to certain death, it is claimed.
he alleged killings happened on a crossing between Nador in northern Morocco and southern Spain in 2014, The Telegraph reports.
Investigators were told that the captain and his second in command, also from Cameroon, believed the weather got worse each time the Christians prayed.
They used planks of wood to beat the Nigerian pastor, with the public prosecutor writing: 'They badly wounded him before throwing him overboard.'
Witnesses claim the duo then searched fellow passengers for signs they were Christian, and similarly attacked five other migrants.
Alain N. B's second in command died before trial could start.
he prosecution state the captain 'was aware that the victims could not possibly survive and that they would die, either by drowning, from the cold, or from the physical injuries they had suffered'.
The sea was rough and there were no boats nearby that could rescue the men thrown overboard.
Just one body, which may have been that of a victim, was recovered.
The trial is happening in Almeria, southern Spain, where prosecutors are calling for six separate terms of 15 years - meaning the captain would be sentenced to 90 years in jail if convicted.
The public prosecutor argues that 'religious motivation' is an aggravating factor.
Sea rescue services rescued 29 survivors from the 10-metre-long inflatable craft, which did not have a motor.
At least 21 people died during the perilous crossing, including seven babies whose mothers had been unable to hold onto them.
All the survivors were from Sub-Saharan Africa, but several appeared frightened of telling authorities what happened.
The two men had €1,500 (£1,287) on their person - the same amount witnesses say their victims were carrying before being forced overboard.