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Officers found the asylum seeker, thought to be from Morocco, after removing several pillows and a black cover from the boot of the car.
Border police discovered the man crammed into the compartment after noticing that the woman driver appeared nervous.
The woman motorist, a Moroccan national legally in Spain, was stopped at the southern port of Algeciras in Cadiz, according to The Local.
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She had taken her car on the ferry from Tangiers, Morocco.
It was not known if the migrant had been injured during the crossing, which can take up to an hour-and-a-half.
The driver and the asylum seeker were both detained at the scene.
The discovery comes after a pregnant Nigerian migrant, was rescued from a dinghy boat as it crossed into the southern Italian island of Lampedusa.
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