Family
The book revolves around the idea of family and around the relationships that are so close that they give the idea of family even if the characters are not related through blood. The idea that family should be above all is promoted since the beginning and families are seen as little cells in a society, structures that support those in them. Jace has a crisis, not being able to connect with his supposed father or with his real one. He believes that if he can’t feel a connection with his father, something is wrong with him. He is shown however that family goes beyond blood and that his family was the Lightwoods all along.
Right vs. wrong
This theme is obvious when analyzing Jace and Clary’s relationship. They are both caught between the desire to be happy and the knowledge that what they are doing is morally wrong. This mental conflict affects them in such a manner that sometimes they can’t bear to be in each other’s presence without feeling pain. Even if it is clear that they won’t be happy unless they are together, they continue to deny their feelings mainly because they are afraid that their relationship will affect those close to them.
Identity
Throughout this book, many of the characters experience realizations about who they are. Jace believes his feelings for his sister, (Clary), make him as evil as their father, (Valentine). The discovery that Valentine injected his son with demon blood only furthers Jace's depiction of himself. Even though Jace fears the elements of his creation, his true self outshines his doubt. Becoming the better and stronger version of Valentine, Jace discovers who his rightful family is as well as his true self.
Overcoming prejudices
The "Downworlders" in this series is a metaphor for oppressed members of society. In this instance, vampires, werewolves, and fairies are seen as lesser citizens because of their demon blood. Despite being equally good people as the Shadowhunters, they are treated differently. In history, minorities have been labeled as unequal to the citizens in the majority. Clare uses the history of minority oppression as inspiration for these characters. At the end of this novel, we see the Shadowhunters and Downworlders setting aside their apparent differences and working together to save their world.