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Gillingham will face either Bristol City or Coventry City in the area final of the Johnstone’s Paint Trophy.
The tie will be over two legs and the aggregate winner will face the northern champions in the final.
Gills boss Peter Taylor knows his team have much to do to make it to Wembley.
He said: “Bristol City have got one of the best squads in the division and to play them over two matches is going to be difficult.
“Coventry, on their day, playing over two matches, that is also going to be difficult. We will just have to see what happens.”
The two sides meet on Wednesday night.
A draw, made behind closed doors, will determine who plays the home leg first. The matches take place on week commencing January 12 and February 2.
“You would love to maybe get an away game first and then finish off a good night here,” said Taylor.
“We are capable of winning against any team in League 1 if we get it right on the day.”
The northern section semi-finals will see the winners of Doncaster and Notts County face Preston while Tranmere host Walsall tomorrow (Tuesday) night.
The Wembley final takes place on Sunday, March 22.