Get the Digi-Egg Of Sincerity. You can now call Submarimon from any dock. The docks are the strange little square things. A "!" will now appear and you can call Submarimon. There are mostly Dolphmon and Gesomon in the Seabeds . Make sure you are at least level 15 before attempting the Seabeds.

In Amaterasu Server, when you go fishing you will probably catch Ebidramon. However, when you get transported by Submarimon, there are mostly MarineDevimon and Dragomon found in the seabeds.