When you have chosen a deity and an alignment for your cleric, you then get to choose two from among the deity's domains. While clerics of a particular religion are united in their reverence for their deity, each religion encompasses different aspects. You can only select an alignment domain (such as Good) for you cleric if his aligment matches that domain.

If your cleric is not devoted to a particular deity, you still select two domains to represent your character's spiritual inclinations and abilities (but the restriction on alignment domains still applies.

Each domain gives your cleric access to a domain spell at each spell level, from 1st on up, as well as a granted power of all the domains selected. With access to two domain spells at a given spell level, a cleric prepares one or the other each day. If a domain spell is not on the Cleric Spell list, a cleric can only prepare it in his domain slot.