South India is more close to the equator than north India,darker skin color is commonly found in peoples living in more southern regions and appears as an adjustment mechanism to hotter climates and greater sunshine. For example southern Europeans are darker in skin color than northern Europeans, though they are not a different race because of this.Skin color evolves after a considerable period of time passed in a certain climate and climate is decided by factors such as exposure to sun-light (temperature), altitude(atmospheric pressure), distance from the equator(humidity) etc. while skin color is not only affected by climate but some other factors too e.g. genes, cultural migrations.
Indian people are strange mix up of different cultures and races but Indian native tribes too were having a lot of diversity in their skin colors due to climate alone although later when invaders who came from better climate for fairer skin color got mixed up with Indian people and added a new variety of fair complexion here.South India is nearer to the equator than northern Indian areas so there is a natural difference between the skin color of north Indian people and south Indian people.
While it has genetically (genes are better proofs than climate or any other factor) been proved that north Indian tribe and south Indian tribe both evolved in locally into Hindu culture then there remains no doubt that color difference also evolved here in India, though later foreigners added a variety of fair complexion here.
The Myth of Aryan Invasion of India