The best price found from United States to Okinawa & the Southwest Islands is on October 31st, 2017, travelling with . See more options, compare prices and book: search flights.
There are flights between major cities in mainland Japan and Amami-Ōshima, Okinawa-hontō (Naha), Miyako-jima and Ishigaki-jima. Kagoshima has flights to/from all these islands and many of the smaller islands as well. Other islands such as Yonaguni-jima and Kume-jima can be reached from Naha or Ishigaki.
Peach Airlines (www.flypeach.com) is a new low-cost carrier that offers cheap deals to Naha and Ishigaki from major cities in mainland Japan.