The 34-year-old man was arrested and faces charges of involuntary manslaughter after his younger brother was found dead inside a suitcase onboard a ferry bound for the mainland from Melilla, a Spanish territory in North Africa.
He raised the alarm about the stowaway's condition when the ferry docked in Almeria after a five-hour trip, but emergency services could do nothing to revive him.
A judge in Almeria ordered that the man, who was not identified, be held without bail after questioning him.
During his court appearance the man said he did not know that his brother, a 27-year-old Moroccan national, was inside the suitcase in the trunk of his car, a court statement said.
In May police discovered an eight-year-old boy from the Ivory Coast curled up inside a suitcase — without air vents — that was being carried across a pedestrian crossing from Morocco into Ceuta, Spain's other north African territory.
His father, a legal resident in Spain, had tried to smuggle the boy into Spain because his income was too low to request residency papers for his son.
The boy was eventually granted temporary permission to live in Spain with his parents.
Each year, thousands of migrants risk their lives trying to enter Ceuta and Melilla, two remnants of the Spain's colonial past which have the European Union's only land borders with Africa, to try to enter Europe.
Many migrants try to scramble over the seven-metre (23-foot) fences that separate the Spanish cities from Morocco while others try to swim or sail from shores on the Moroccan side.
Four migrants died on Sunday after trying to swim around a maritime fence separating Ceuta from Morocco.