What does Matthew 3:9 mean?

Israel's religious leaders are hearing a warning: God's coming judgment is coming against them. John the Baptist now adds that they have made a wrong assumption about how God will deal with His people Israel. They had been operating under the idea that God would not focus His wrath on Israelites, the children of Abraham.

Israel's religious leaders, of all people, should have known better. Throughout Israel's history, God had brought judgment on His chosen people for their unfaithfulness to Him. He had always saved a remnant: a small proportion of the people. He had never broken any of His eternal promises to the nation, but that did not keep God from bringing judgment on most of the Israelites living at any specific time.

John's warning, though, goes beyond that simple truth. He tells the Pharisees and Sadducees not to presume that the arrival of the kingdom of heaven means they will not be judged. While it is true that God will save a remnant of Abraham's seed, John adds a curious statement: God is able to raise up new children of Abraham even from these stones. He may have been pointing to the stones in the Jordan River. This is wordplay. In both Greek and Aramaic, the word for stones is very close to the word for children.

John's statement goes beyond suggesting that God will spare a remnant of the biological children of Abraham from His judgment as He sets up His kingdom. In truth, through the coming of Jesus as King, God will add those who trust in Christ to Abraham's line even though they are not directly descended from him. This parallels Jesus' statement in a later argument with the Pharisees (John 8:31–38).