Charles V was born when the Hapsburg royal family and the Spanish royal family intermarried, producing a new dynasty-- the Spanish Hapsburgs.  Philip I, of the Hapsburgs, and Joanna of Castile, from Spain, gave birth to Charles V, Ferdinand I, and three girls. 

The original Hapsburgs were based in Germany, and Charles' brother Ferdinand continued the family control of that area after Charles' death.  Charles' son Philip II contined the Spanish Hapsburg dynasty.  Becuase of this family division of power, two seperate lines of the family tree were formed-- the Spanish and the German Hapsburgs.