The baobabs are giant plants that grow on the prince’s planet. They start off as tiny weeds, but if not uprooted and discarded when they are little, they firmly take root and can even cause a planet to split apart. The prince tells the narrator:
“It is a question of discipline….When you’ve finished your own toilet in the morning, then it is time to attend to the toilet of your planet, just so, with the greatest care. You must see to it that you pull up regularly all the baobabs, at the very first moment when they can be distinguished from the rose-bushes which they resemble so closely in their earliest youth…” (5.16).
On a metaphorical level, the baobabs stand for unpleasant things in one’s nature – if we don’t spot them and weed them out early, they will take firm root and distort our personalities.
According to some literary critics, the baobabs have another, darker meaning, too: they can be interpreted as “visual metaphor[s] for Nazism” (source). This comparison makes a lot of sense, especially when you consider that Saint-Exupéry fought in World War II against the Nazis, and that the Nazis were still rising to power when The Little Princewas written.
If the Nazi comparison holds, then the prince’s comment about the baobabs looking so similar to rose bushes becomes especially poignant. He says that baobabs “‘resemble [rose bushes] so closely in their earliest youth…’” (5.16). So, at the very beginning of something, you can’t tell the good from the bad. The rose bushes and the baobab growths look the same. But one will grow up to be beautiful and one will grow up to be disastrous. Similarly, the Nazis started out like many other political parties—but, left alone, they grew to tremendous power and caused unbelievable, inhuman damage.