A communication system, a relay device, and a communication method are provided in a configuration where multiple communication devices are divided into multiple groups, a relay device is provided for each group, and the relay device relays data exchanges between groups. The data that is exchanged between a second relay device and an external wireless communication device is stored such that it is distributed among multiple databases of first relay units. Data received from the external communication device is stored in an individual region in the database of the first relay device and a data storage destination table in the second relay device is encrypted. If the first relay device stores data received from an ECU in the database, the second relay device is notified, and the second relay device updates the data storage destination table according to the notification.