“At the time of its bombing, Hiroshima was a city of both industrial and military significance. A number of military units were located nearby, the most important of which was the headquarters of Field Marshal Shunroku Hata’s Second General Army, which commanded the defense of all of southern Japan,[102] and was located in Hiroshima Castle. Hata’s command consisted of some 400,000 men, most of whom were on Kyushu where an Allied invasion was correctly anticipated.[103] Also present in Hiroshima were the headquarters of the 59th Army, the 5th Division and the 224th Division, a recently formed mobile unit.[104] The city was defended by five batteries of 7-and-8-centimeter (2.8 and 3.1 in) anti-aircraft guns of the 3rd Anti-Aircraft Division, including units from the 121st and 122nd Anti-Aircraft Regiments and the 22nd and 45th Separate Anti-Aircraft Battalions. In total, over 40,000 military personnel were stationed in the city.[105]”
“The city of Nagasaki had been one of the largest seaports in southern Japan, and was of great wartime importance because of its wide-ranging industrial activity, including the production of ordnance, ships, military equipment, and other war materials. The four largest companies in the city were Mitsubishi Shipyards, Electrical Shipyards, Arms Plant, and Steel and Arms Works, which employed about 90% of the city’s labor force, and accounted for 90% of the city’s industry.[166] Although an important industrial city, Nagasaki had been spared from firebombing because its geography made it difficult to locate at night with AN/APQ-13 radar.[108]”
Odd; my understanding was that the cities were chosen because they wouldn’t be defended. They didn’t want Enola Gay or Bock’s Car shot down.