Elias is come already - That is, John the Baptist has come, in the spirit and power of Elias. See Luke 1:17.
They have done unto him whatsoever they listed - The word "list" is an old English word, signifying to choose, to desire, to be inclined. See Judges 3:8. It means, here, that they had done to John as they pleased; that is, they had put him to death, Matthew 14:10.
Mark adds Mark 9:12 that Jesus told them that it was "written of the Son of man that he must suffer many things, and be set at naught." This was written of him particularly in Isaiah 53:1-12. To be set at naught is to be esteemed as worthless or as nothing; to be cast out and despised. No prophecy was ever more strikingly fulfilled. See Luke 23:11, Luke 23:14-21. This narrative, with some additions, is found in Mark 9:14-29, and Luke 9:37-43.

Knew him not - Or, ουκ επιγνωσαν αυτον, They have not acknowledged him. That is, the Jewish rulers have not acknowledged him, did not receive him as the forerunner of the Messiah. But it appears that all the rest acknowledged him as such; and some, from the power and demonstration of his preaching, were inclined to think he was more, even the Messiah himself: see Luke 3:15.

But I say unto you,.... A way of speaking used by Christ, when he opposes and contradicts any of the tenets of the Scribes and Pharisees; see Matthew 5:22 "that Elias is come already"; the person that was signified by, and prophesied of, under the name of Elias: for Christ refers not to the late appearance of Elias on the mount, but to the coming of a certain person some time ago; who came in the power and spirit of Elias, and was the forerunner and harbinger of him, the Messiah; as was said of him he should, "and they knew him not"; that is, the Scribes and Pharisees, who believed that Elias would come before the Messiah; and yet when he who was designed by him was come, they knew him not, they did not know him to be the Elias; they knew him under the name of John the Baptist, and seemed pleased with his ministry for a while, but afterwards rejected his doctrine and baptism, which is referred to in the next clause:
but have done unto him whatsoever they listed; they did not believe what he said, nor repent upon his preaching to them; they rejected the counsel of God he declared, not being baptized of him; they treated him with indignity and contempt, charging him with having a devil, and were well pleased when Herod put him to death; some of whom were doubtless among those that sat at meat with him; for whose sake, as well as for his oath's sake, he ordered the execrable murder to be committed:
likewise also shall the son of man suffer of them. Christ takes this opportunity to confirm what he had said in the preceding chapter, concerning his sufferings and death; and his meaning is, that as sure as John the Baptist had suffered indignities, and death itself, so sure should the son of man suffer like things; if not from the same individual persons, yet from that generation of men.

Elijah is come already - And yet when the Jews asked John, Art thou Elijah? He said, I am not, John 1:21. His meaning was, I am not Elijah the Tishbite, come again into the world. But he was the person of whom Malachi prophesied under that name.