Excellent question. Of course, when we think of the theme of any given work of literature there are an entire range of answers that can be given. However, certainly when we consider this excellent tale, one of Poe's true classics, we cannot fail to ignore the treatment of evil in this story and the way that Roderick and Madeline are subject to a terrible "curse" in the words of Roderick.
One of the most ironic moments in the tale is when the narrator with Roderick entombs the "corpse" of Madeline, and points towards her resurrection by describing her body:
The disease which had thus entombed the lady in the maturity of youth, had left, as usual in all maladies of a strictly cataleptical character, the mocker of a faint blush upon the bosom and the face, and that suspiciously lingering smile upon the lip which is so terrible in death.
This of course, with hindsight, indicates that Madeline is still living, as the narrator and Roderick will discover together later on.
The main form of symbolism in the story is the way that the House of Usher is used to symbolise the actual decay and rot that is present in the family of Usher. Consider how the narrator describes the House as he comes upon it at the beginning of the tale:
In this there was much that reminded me of the specious totality of old wood-work which has rotted for long years in some neglected vault, with no disturbance from the breath of the external air.
Of course, the shared fate of the House and its descendants indicates some kind of mystical, abstruse link between them that unites them in their destruction. The theme of some kind of indescribable and unexplainable evil is therefore referred to through the irony of Madeline's "death" and her subsequent resurrection, and the grisly end that greets both the house and its two descendants.