Um, Mr. Scott? Do you know how to spell? It's alchemist, not alchemyst.
Sorry, Shmoopers, the dude knew what he was doing. Alchemyst is simply an old timey way of spelling alchemist, and that old timey spelling reflects the fact that the alchemyst in question is—you guessed it—very old.
So who is "the Alchemyst" of the title? Why, Nicholas Flamel, of course. And in real life, this guy was indeed an alchemyst in ye olden times—fourteenth century France to be exact.
What's that? Oh, sorry Nicholas. We know you're not just any alchemyst, you're the Alchemyst—the most important sciencey magician (or is it magicky scientist?) that ever lived. And just how did this guy become the most important alchemyst of all time? You'll have to check out 4.42 for the answer. We would never reveal a magician's secrets.
The alchemyst stands in contrast to Dr. John Dee, who, is known to dabble in alchemy himself. Although he's a super powerful magician and necromancer (a sorcerer who can raise the dead), he's not as skilled as his more benevolent counterpart, and he's got some suspicious motives behind his actions. Because he's not the alchemyst, and because he's standing in our alchemyst's way, we know that this dude is a big fat villain.
In this sense, the title reminds us who to root for as we read. This novel is the story of the alchemyst—Nicholas Flamel, as he fights foes and tries to survive. Of course the next book in the series is called The Magician. Gee, whom might that refer to?