There was no mention of MK Dons on the front of AFC Wimbledon's matchday programme when the two sides met in September
AFC Wimbledon have been charged with a breach of English Football League regulations following their home match against MK Dons on 22 September.
Wimbledon referred to the away side as Milton Keynes or MK, and did not mention them on their programme cover.
The EFL had said it "sought assurances" from Wimbledon before the League One game to ensure it would be "treated in a consistent and appropriate manner".
Wimbledon are yet to decide how they will respond to the charges.
The south-west London club are accused of 'breaching Regulation 3' of the EFL's rules, which say no member should "unfairly criticise, disparage, belittle or discredit" any other club in the league.
Wimbledon had also failed to recognise the MK Dons' name in their very first league meeting at Kingsmeadow, which took place in March this year.
The case will be heard by an independent panel.
AFC Wimbledon did not acknowledge the 'Dons' parts of MK Dons' name on their scoreboard when the teams met at Kingsmeadow in MarchTwo clubs bound by a turbulent history
AFC Wimbledon were formed in 2002 by Wimbledon FC supporters who were upset by the Football Association's decision to allow their club to move to Milton Keynes.
The old Wimbledon FC, nicknamed the Dons, relocated to Milton Keynes in September 2003 and subsequently changed their name to MK Dons in the summer of 2004.
Meanwhile, AFC Wimbledon won five promotions in nine years to reach the Football League in 2011, and won promotion to League One - the same division as MK Dons - in 2016.
The two clubs first played each other in the FA Cup in December 2012, with six meetings in all competitions. September's fixture was the second time AFC Wimbledon have hosted MK Dons.
AFC Wimbledon have recently been given permission to build a new stadium on Plough Lane in Merton, an area they see as the club's spiritual home.
Source: bbc.com