I know it was her Patronus. But. As JKR stated in an interview:  Chely: James patronus is a stag and lilys a doe is that a coincidence? J.K. Rowling: No, the Patronus often mutates to take the image of the love of one's life (because they so often become the 'happy thought' that generates a Patronus).  Meaning Lily's Patronus does not represent her personality as Snape knew it. Apparently Lily's Patronus would be (or was - if she mastered it earlier) something different, more personal. Obviously Snape's Patronus should have changed together with Lily's from being something different before (if he could cast it by the time). Doe is the evidence of Lily's love for Snape's worst enemy - probably the worst thing happened in Snape's life apart from her death. How does this represent the happiest thoughts for Snape? Basically, Snape's Patronus mutates to match James's - which is just bizarre, especially when you think that Snape should be aware of it. Side thoughts: Patronus probably should not necessarily take form of your love's Patronus to match. We see Tonks cast a wolf when fall in love with Lupin - probably just because a wolf is something that associated with him in her mind. I doubt that Lupin's Patronus is a wolf, given he should consider it to be the most hated part of himself. So Patronus should be more about your own perception of the loved one (speculative though). So... why a doe?!
Why is Severus Snape's Patronus the same as Lily Potter's? Are Snape and Lily related somehow? Are Snape and Harry related?
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