The theme of parents being replaced or deposed by their children is central to the story. King Philip claims to not trust his son with matters of state because he is hotheaded and will get into trouble, but there are potentially other worries in his mind. Philip usurped his father's throne, and he fears that his son will do the same. Additionally, and more twisted than the first example, Don Carlos is in love with his father's wife and wishes to replace him by taking her for his own.

The theme of forbidden love is also prominent. Several characters in the work have an unrequited affection for another character. Don Carlos is infatuated with the Queen, Elizabeth de Valois, whom he courted prior to his father taking her as his own wife. Because of her position and loyalty to (or fear of) the King, she refuses to be with him, even though he entreats her frequently and asks to make her his mistress. On the other hand, Princess de Eboli is in love with him, but he rejects her advances because he is obsessed with the Queen.

Throughout the story, there is an undercurrent of sedition and espionage. Obviously, the king fears his son will usurp him and take his throne, so he is constantly worrying about espionage, but there is more. The spurned lover, Princess de Eboli, plans a trap with some other members of the nobility for Don Carlos. She and the Marquis lead him into a trap and have him imprisoned, although this ends up increasing his support in the nation.