The Underwater Pen is an inventory item obtained in the main story in both Endless Ocean games. This item enables the player to suspend colored particles in the water, leaving marks as directions, temporary graffiti, or to unlock more information about creatures.

Some fish respond to the Pen more than they respond to other stimuli, like petting or Food, and swim around in the drawings the player leaves behind. In the first Endless Ocean, some deep-sea creatures are notable examples of this phenomenon, like the Fanfin and the Pelican Eel, which are both only unlocked once the player uses the Pen near them and they get the chance to swim around in the markings.

The Pen uses five colours: red, yellow, green, blue, and white. There is not a way to unlock more pen colours.

The marks made by the Underwater Pen only last for one dive, and they disappear whenever the player returns to the boat.

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