Chester City have been wound up by the High Court yesterday while Blue Square North side Farsley Celtic were disbanded.
126-year-old club Chester, who were kicked out of the Football Conference on 26 February, owed HM Revenue & Customs £26,125 in unpaid taxes.
Chester supporters group City Fans United now intend to start a new 'phoenix' club in a lower league and have already put in an application to the Football Association for a licence.
An FA spokesperson said in a statement on Wednesday afternoon: "The FA notes today's decision of the High Court in relation to Chester City.
"The winding-up of any club is a loss to the game and in particular to the supporters of that club. In order to maintain a senior football club in the city of Chester, The FA will welcome applications if the club wishes to reform.
"Any such applications will be considered by The FA's Leagues Committee."
The CFU, who hope that City can reform at Unibond League level, have also rapidly distanced themselves from an application made by Chester to join the Welsh football system.
"We understand that was a last-ditch effort by our former owner Stephen Vaughan to keep hold of the club," CFU spokesman Jeff Banks told BBC Sport.
"But we would have had to have started at the very bottom.
"And it would have been rejected out of hand in any case by our local council, who say we are an English club and should be playing in an English league.
Farsley Celtic were disbanded after the club's administrators rejected numerous improved offers from the Palmer-Farrell consortium.
Their expulsion from the Football Conference was expected to occur later this week after they failed to fulfil their last three fixtures. The Blue Square North side entered administration at the start of the season with reported debts of £750,000. The club are expected to reform next season in the Unibond First Division.