This gets asked here fairly often -- you may be interested in this section of our FAQ. The tl;dr is that the American strategic bombing campaign had already destroyed most of the major cities in Japan, including most of Tokyo, by firebombing, and Hiroshima was one of several cities on a "reserved" list of cities spared firebombing for testing the atomic bombs. Nagasaki was actually a secondary target, which had been conventionally bombed, that was hit after the primary target of the mission, Kokura, was found to be obscured by smoke.

This answer in particular goes over the target list history basics, including the non-targeting of Kyoto (which was the Army's preferred primary target, but was eliminated from the target list at the intervention of the Secretary of War and President Truman).

There's always more to be said, so feel free to ask.