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The Japan Airline (JAL) Group and the All Nippon Airways (ANA) Group are the predominant airlines consisting of smaller carriers for domestic flights and serve over fifty cities. The JAL Group includes Japan Airline (JAL), Japan Air System (JAS), JAL Express and J-Air and the ANA Group includes ANA and Air Nippon. Some of the several small independent domestic carriers include Skymark Airlines, Air Do, Fairinc, most of which specialize in a certain local destination or big cities.

Japan Airlines (JAL) is known as the largest airline company not only in Japan but in entire Asia. The Japan Airlines Corporation consists of two airline companies: Japan Airlines International that is based at two local international airports, Narita Airport (Tokyo) and Kansai Airport (Osaka) and Japan Airlines Domestic that is based at the Haneda Airport (Tokyo) and Itami Airport (Osaka). Eight other airlines belonging to the Japan Airline (JAL) Group are: Harlequin Air, Hokkaido Air System, JAL Express, JAL Ways, J-Air, Japan Air Commuter, Japan Asia Airways, and Japan Transocean Air. Japan Airlines International's route covers a vast area on the globe.

All Nippon Airways (ANA), Japan's second-largest airline company after Japan Airlines used to be Japan's largest domestic airline. ANA's international and domestic hubs are the same as those of Japan Airlines and are in Tokyo and Osaka. Both Nippon Cargo Airlines (NCA) and Air Nippon are ANA's affiliated companies providing charter flights, and Air Next was established to handle flights from Fukuoka Airport. The Chubu Centrair International Airport (Nagoya) and the New Chitose Airport (Sapporo) are the secondary hubs for ANA.