In The Scarlet Letter flowers are used often as a way to symbolize various themes and ideas. The rosebush growing by the prison illustrates how even though Hester is in jail, being judged for something bad, there is still beauty in her soul - her character is beautiful. Later in the novel, Roger Chillingworth, Hester’s husband is talking to her about judgment, revenge and pity. Hester tells him that she pities him for he has changed so much:
And I thee,” answered Hester Prynne, “for the hatred that has transformed a wise and just man to a fiend!
My old faith, long forgotten, comes back to me, and explains all that we do, and all we suffer. By thy first step awry, thou didst plant the germ of evil; but since that moment, it has all been a dark necessity. Ye that have wronged me are not sinful, save in a kind of typical illusion; neither am I fiend-like, who have snatched a fiend's office from his hands. It is our fate. Let the black flower blossom as it may!
There is a metaphor in this paragraph. Chillingworth tells Hester that her adultery has "planted the germ of evil" that has transformed his soul from light to dark. So when he says "let the black flower blossom as it may" he is referring to his tortured soul, that has become black. What has turned him black is his hidden sin of trying to torture Dimmesdale, the father of Hester's child, Pearl. Instead of trying to forgive Hester AND Dimmesdale, Chillingworth puts himself in the place of God, seeks vengeance on his own, and is destroyed by the black sin in his heart, because God says, "Vengeance is mine." Since this is a novel with Puritan themes, the author is showing the destructive nature of sin, and hidden sin is the worst because it is not acknowledged so that it can be forgiven.
Read about it here on enotes.