An historic first meeting between the two sides could take place in the second stage of England's primary cup competition, should they win their respective replays
The Dons were formed in 2004 following Wimbledon FC's financial woes and subsequent administration. Yet controversy surrounded the side when they laid claim to the history of Wimbledon FC despite a counter-argument from the Milton Keynes boardroom that they were an entirely new club.
After the relocation and re-branding of the club, fans established AFC Wimbledon - and they are in line to face MK Dons if the pair manage to secure victory in their first round replays against Cambridge and York respectively.
The draw has also produced a number of all non-league fixtures, guaranteeing that at least three teams from the Conference National and below will be competing in the third round.
The lowest ranked side Hastings United, who currently ply their trade in the Isthmian League Premier Division, will play fellow semi-professional outfit Harrogate Town, while Dorchester Town face a trip to either Luton Town or Nuneaton Town.
Macclesfield travel to one of Guiseley or Barrow to complete the fixtures which guarantee non-league representation in round three.
Second round ties will be played during the first weekend of December.
Full fixture list:
Preston North End v Gillingham
Bury v Southend United
Sheffield United v Port Vale
Carlisle United v AFC Bournemouth
Crewe Alexandra v Burton Albion or Altrincham
Northampton Town or Bradford City v Brentford
Luton Town or Nuneaton Town v Dorchester Town
Alfreton Town v Gloucester City or Leyton Orient
Oldham Athletic v Doncaster Rovers
Braintree Town or Tranmere v Chesterfield
Rotherham United v Notts County
Cheltenham Town v Hereford United
Guiseley or Barrow v Macclesfield Town
Accrington Stanley v Oxford United
Lincoln City or Walsall v Mansfield Town or Slough Town
Harrogate Town v Hastings United
Coventry City v Morecambe or Rochdale
Cambridge City or MK Dons v York City or AFC Wimbledon
Crawley Town v Chelmsford City
Fleetwood Town v Aldershot Town