The rescue service says it collected 25 migrants before dawn today from one boat and 19 others hours later from a second craft. No casualties were reported.
It says captains of passing vessels reported the migrants approaching Spain's southeast coast overnight.
The Spanish Red Cross says those aboard both rescued vessels have been examined at the port of Almeria and are unhurt.
The International Organization for Migration says Spain received about 3,850 migrants via sea crossings and rescues in 2015. Others seek asylum in Spain via its North African enclaves, Melilla and Ceuta.