Media-Most last month concluded a deal with the Russian state gas company, Gazprom, to liquidate its substantial debts.
Earlier the office of the Russian prosecutor-general announced efforts to seize Mr Gusinsky's property abroad.
Russia's Interfax news agency quoted court authorities as saying that the request to liquidate the Media-Most empire was filed on 9 December.
The Russian media baron is fighting extradition to Russia from Spain where he was arrested on fraud charges.
His NTV television channel has been a frequent critic of Kremlin policy, especially over the war in Chechnya.
Mr Gusinsky has dismissed the charges against him as a pack of lies, saying he is a victim of political persecution.
He alleges that the Russian Government is trying to smash the independence of his media empire.
Substantial debts
Among the individual companies named in the Media-Most bankruptcy suit are the NTV channel, and the Seven Days publishing company.
Media-Most last month concluded a deal with the Russian state gas company, Gazprom, to liquidate its substantial debts.
Gazprom agreed to take a part-share in the group.
Media-Most denies having any further unpaid debts.
The Director-General of NTV, Yevgeny Kiselev, described the court action as an attack on what is left of democracy in Russia.
Jail sentence
Prosecutors in Moscow have rejected Mr Gusinsky's claims that he is being persecuted for political reasons, insisting that the tycoon is wanted for fraud.
Spanish lawyers are warning that the extradition process may take several months because there is no formal extradition treaty between Spain and Russia.
Mr Gusinsky has not returned to Russia since July for fear of being arrested, having spent three nights in jail earlier in the year following his arrest concerning fraud in a privatisation case dating back to 1997.
Mr Gusinksy, aged 47, faces a minimum jail sentence of six years if convicted of fraud.
President Putin has sought to dispel fears that a political vendetta is being waged against Mr Gusinsky, saying he is in favour of a free press.