Cubits are the main form of premium currency within the game. It is often found as a small reward for completing many tasks and missions and can also be received by exchanging stored Water. Cubits are used to purchase, as well as to advance and upgrade, ships, items and ammunition from the Fleet Store. It is the only virtual currency of the game which can be directly purchased with real life money.
Cubits - High value currency
"Currency that can be exchanged for advanced items and other resources."
While Merits are mostly given as an award for participating in Player vs Player combat, it can also be used as a highly valued premium currency to purchase nuclear ammunition, advance multi-class ships, purchase and advance Carrier class ships as well as upgrade ship role abilities.
Merits - Special awards for combat performance
"Awarded for exceptional performance in the service of your fleet. Merits can be earned by completing the Disrupt Enemy Operations assignment and defeating enemy players and Outposts."
The resource Tylium can also be considered a form of currency as it can be used to purchase ships, items and upgrade ship equipment.