Magic vs real, pre-colonization vs post-colonialization, nature vs modernity. These seem to be some of the major themes of "Cien Anos de Soledad". The story thus far, as I understand it, is a retelling of the colonization of the Americas. The Buendia family has settled in a beautiful and somewhat primitive place called Macondo, etc.
What I found more interesting was the incorporation of Christian ideals into the story, which also played an immense roll in the colonization of the americas (the spanish viewed the indigenous people as barbaric and unintelligent because of their lack of worship for the christian god). The story of genesis is apparent in "Cien anos de soledad" as well as christian ideals such as keeping blood lines clean.
I think that Garcia Marquez's focus on christianity in the plot may be part of the reason he uses magic in his novel. Christianity is not real to the people of latin america just like magic is not real in the world. If christianity can be real, magic can be real? I am almost reading the use of magic as a coping mechanism for a religion that was brutally forced upon a population. It is how individuals experienced la conquista. It is also perhaps to emphasize the idea of how the europeans invading the western world must have appeared to the indigenous: like magic.