Why did they choose those two cities to drop the atomic bombs on?

Lists of Japanese cities eligible to bet A-bomb targets were made up by Leslie Groves for the Secretary of War Stimson. Groves wanted cities that had not been heavily damaged by U.S. B29 raids so that the level of damage created by the A-bomb could be accurately studied. Stimson wanted to spare cities that had great cultural value (that dropped Kyoto off the list). Hiroshima & Nagasaki fit the above categories and had some token military facilities to help validate them being used as targets.