Deception and self-deception
Almost every major event in the play depends on someone believing something false. Don John uses deception to destroy Hero. Don Pedro uses it to help Beatrice and Benedick. The play keeps asking whether the characters are deceived by others or by their own wishes.
Honor and reputation
In Messina, reputation is everything, especially for women. Hero loses her standing the moment Claudio accuses her, regardless of evidence. The play shows how fragile reputation is and how little it takes to destroy it.
Love and pride
Beatrice and Benedick both use wit and pride as armor against vulnerability. Their love plot is about what happens when that armor cracks. They cannot admit their feelings until they believe the other person already feels the same.
Gender and power
Men in this play control women's fates. Leonato can give Hero to Claudio. Claudio can destroy her with an accusation. Beatrice has more freedom because she is a wit, not a prize, but she still needs Benedick to act on her behalf when Claudio wrongs Hero.
Appearance versus reality
Characters constantly mistake what they see and hear for the truth. The masked ball, the staged conversations, and the window scene all depend on the gap between what appears to be happening and what is actually happening.