A subclass in Phantasy Star Online 2 is a second class chosen to augment a character's main class.

The skill tree and photon arts of the subclass become fully usable, but some skills and photon arts may function with a type of weapon normally restricted to the main class, requiring use of a rare weapon without normal class restrictions. If the subclass is force or techer, the character will be able to use techniques through the subpalette, regardless of weapon. For example, a HU/RA can still only equip the few rare assault rifles and launchers a hunter could normally equip, but when doing so, is able to use assault rifle or launcher photon arts due to the ranger subclass.

Subclassing becomes accessible by completing Subclass License upon reaching level 20 in any class. Like the main class, subclass can be changed between quests at the class counter in the gate area of the Arks lobby free of charge. An additional 10% of any earned experience is provided to the subclass if it is below level 45.

20% of the subclass's stats are also added to the character's base stats. If the subclass level is higher, subclass stats are capped at the current main class level. For example, a level 1/65 HU/RA has the same base stats as a level 1/1 HU/RA. When the hunter class reaches level 2, the character will then have the same base stats as a level 2/2 HU/RA, and so on.

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