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In both of these verses you mentioned, it is John the Baptist speaking of the Lord Jesus Christ.  Let’s read Matthew 3:11-12, “I indeed baptize you with water unto repentance: but he that cometh after me is mightier than I, whose shoes I am not worthy to bear: he shall baptize you with the Holy Ghost, and with fire: Whose fan is in his hand, and he will throughly purge his floor, and gather his wheat into the garner; but he will burn up the chaff with unquenchable fire.”  John humbly admits that Christ is far greater than he.  John baptized with water; Christ is the one who will baptize with the Holy Spirit and fire.

John the Baptist was the fore-runner of Christ.  His baptism was one of repentance.  While the mode of immersion is the same as Christian baptism, the purpose of his baptism was different.  Those baptized of John were showing repentance for their sins.  Christian baptism is not unto repentance, it is a baptism unto Christ’s death who has taken our place and died for us.  Romans 6:3-5 says, “Are you ignorant that we, as many as have been baptised unto Christ Jesus, have been baptised unto his death? We have been buried therefore with him by baptism unto death, in order that, even as Christ has been raised up from among the dead by the glory of the Father, so *we* also should walk in newness of life. For if we are become identified with him in the likeness of his death, so also we shall be of his resurrection.”

So, what did John mean when he said that Christ would baptize with the Holy Ghost and with fire?  It is important to understand that John’s words refer to the first and second coming of the Lord.  The first is a baptism of blessing; the second is a baptism of judgment.  If we are clear about this, understanding his words will be simple.  The truth that Christ would baptize with the Holy Ghost is in connection with His first coming.  The Lord Jesus, after His resurrection and prior to His ascension to Heaven said in Acts 1:5, “For John truly baptized with water; but ye shall be baptized with the Holy Ghost not many days hence.”  This baptism occurred on the Day of Pentecost; when God’s Spirit came down to indwell every believer.  We read in 1 Corinthians 12:13, “For by one Spirit are we all baptized into one body, whether we be Jews or Gentiles, whether we be bond or free; and have been all made to drink into one Spirit.”

The truth that Christ would baptize with fire is in connection with His second coming at the end of the Tribulation Period, when He comes to judge all nations.  This is what John was speaking of in Matthew 3:12 when he said, “Whose fan is in his hand, and he will throughly purge his floor, and gather his wheat into the garner; but he will burn up the chaff with unquenchable fire.”  Some have taught that the baptism with fire refers to the tongues of fire that appeared when the Holy Spirit came down on the day of Pentecost in Acts 2:1-4, but considering John’s words here, we see that he is linking fire with judgment, not blessing.  (103.4)