you'll find some information in these posts
links to posts about alternate targets: Why did the U.S. military decide to drop atomic bombs on Nagasaki and Hiroshima but not on the largest cities like Tokyo?, and Which city would the U.S. target in a third nuclear strike against Japan?
For this question you need /u/restricteddata but until he shows up here is his answer from the FAQ
You can read the account of the original target selection meeting, May 1945, here: http://www.dannen.com/decision/targets.html Short answer: the cities chosen all had some sort of strategic value, but were mostly chosen in order to display the power of the bomb on a civilian population. This meant they had to be relatively built-up, and had to be not already firebombed. The cities were placed on a "reserved" list to be untouched by firebombing. Kyoto was dropped from the list on the request of Secretary of War Stimson because of its cultural value. Nagasaki replaced it. Nagasaki was not the primary target on August 9th, however — Kokura was, but they couldn't get a good visual on the target because of the clouds, and they had been explicitly told not to bomb without visual confirmation. They headed to Nagasaki, where there were also clouds, but a break occurred just at the last possible moment, allowing them to drop the bomb and head back. The Nagasaki mission was a bungle in many ways; they missed the actual aiming point, they almost ran out of fuel, they failed to rendezvous with observation planes, and other mishaps.
If /u/restricteddata does show up somebody remind him that he still owes me a good write-up on how Nagasaki came to be chosen as a target.
Hiroshima was the location of the Ujina Port and several large supply depots. It was one of the largest shipping centers in the entirety of Japan at the time. It was also the Headquarters of the [2nd General Army](http://en.wikipedia.org/wiki/Second_General_Army_(Japan) and the Army Marine Headquarters.
Nagasaki was also a major port city, and had been for several centuries. In fact, most of the trade the country did with the western world was through Nagasaki. Being one of the most important Ports in the country; during WWII a massive naval base was stationed there.
Both cities had large populations, (Hiroshima, half a million, and Nagasaki, quarter million), steel and metal working plants, drydocks, and engine factories. This, combined with their proximity to allied controlled islands made them perfect targets.