The best price found from United States to Okinawa & the Southwest Islands is on April 3rd, 2019, travelling with Alaska Airlines. See more options, compare prices and book: search flights.
There are flights on Japan's big two airlines, Japan Airlines (JAL) and All Nippon Airways (ANA) between major cities in mainland Japan and Amami-Ōshima, Okinawa-hontō, 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. In recent years, a number of low-cost airlines have commenced services from a variety of cities into Naha and a handful of other island destinations. It pays to shop around and explore different route combinations before you travel.