The pair were arrested at around 3.30pm on Tuesday, Spain's 20 minutos newspaper reported.
The search for the mother and her partner began after a forensics examination on a dead two-year-old whose body was discovered on November 3rd in a suitcase near train lines in the La Argañosa neighbourhood of the Asturian capital of Oviedo.
An autopsy revealed signs of a violent death with police suspecting murder.
The search for the child's parents was stepped up after police were given information they were in León, with the arrests coming shortly after the baby's father called the emergency services number saying he wanted to hand himself in.
The mother and father are now set to appear before a magistrate.
Police sources said recently that railway workers discovered the the child's body while weeding alongside railway tracks. When they approached the piece of luggage they discovered there was something next to it wrapped in fabric.
It was then they saw the foot of the child.