This story by Poe is one of sheer terror because it concerns a man who is at the mercy of other people. The narrator has been accused of something by the Spanish Inquisition and is being tortured to confess. The horror continues because the man will feel that he his agony will be over by dying, but then he'll wake up again and some new torture awaits him. He is tortured, then revived, then tortured again - horrible mental games are played upon him.
As far as a theme, I would say that the theme of this story is the horror of torture and being at the mercy of cruel people. Fortunately, the man is saved at the end when Toledo is captured, but he has to undergo some horrible things prior to this happening. His isolation and utter dependence on other people is definitely a theme within this story that should be further explored in a close read of the tale.
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I think another theme might follow more along the lines of the Spanish inquisition (spelling sucks sorry) showing how Catholosism is slowly "cutting" ( in the pendulum sense) away at other religons (jewish) this would be shown as a motif and could possible be built off as a secondary theme. But listen to the expert im just contributing my two sense