The outspoken critic was shot dead by unidentified gunmen in his car on the outskirts of Banjul in December 2004.
The court in Banjul also separately issued an arrest warrant for ex-interior minister Ousman Sonko over the death of former intelligence chief Daba Marenah.
Hydara, 65, an outspoken critic of then president Yahya Jammeh, was shot dead by unidentified gunmen in his car on the outskirts of Banjul in December 2004.
He was the editor and co-founder of the independent newspaper The Point and a one-time Gambia correspondent for Agence France-Presse (AFP).
Jammeh, whose regime was accused of numerous human rights violations, went into exile at the end of January after more than 22 years in power following his defeat in December's presidential election by Adama Barrow.
Police prosecutors Thursday charged former colonel Kawsu Camara and major Sanna Manjang, an army deserter, with "murder and conspiracy" over the killing of Hydara, a judicial source told AFP.
It is the first time authorities have openly linked the pair to the killing.
The two men are however long believed to have been members of Jammeh's ultra-loyal death squad, known as the "Jungulars", which has been accused of carrying out extrajudicial killings and torture by the United Nations and rights groups.
Police asked the court in Banjul to issue arrest warrants for the two men after they were charged, the source said. Principal Magistrate Isatou Janneh agreed to the request.
"The Gambian authorities will present the arrest warrant to Interpol or the country where they are hiding for them to be extradited to Gambia," the source said.
Manjang left the Gambia for Guinea-Bissau the day that Jammeh went into exile after contesting the election results for six weeks.
In 2009, Camara was arrested and charged with treason over a failed coup, along with former defence chief Lang Tombong Tamba and other soldiers. He was convicted and sentenced to death in 2010 but his sentence was later commuted to life imprisonment.
Jammeh pardoned Camara in 2015 and he left for Senegal.
The magistrate also issued an arrest warrant for Sonko and eight other suspects over the death of Marenah, former director of the National Intelligence Agency, another judicial source said.
After he was sacked in September 2016, Sonko fled to Sweden and then Switzerland, where he is currently being held in a crimes against humanity probe.
Sonko has been accused of overseeing and committing torture while heading the interior ministry from 2006 to 2016.
The other suspects named in the arrest warrant include general Bora Colley and other army officers.
The suspects are accused of being involved in the deaths of Marenah and several other people who were believed to have been executed.
Marenah has been missing since his arrest in March 2006, along with several soldiers, over an alleged coup attempt. The government had claimed they escaped while being transferred from the State Central Prison on the outskirts of Banjul to another jail.
The government of new President Barrow has said a body will be set up to investigate forced disappearances in the small west African nation.