Zaur Dadayev and Anzor Gubashev have been charged in connection with the murder of Russian opposition activist Boris Nemtsov.
The Moscow court said one of the men, Zaur Dadayev, had admitted involvement in the shooting on a bridge near the Kremlin on February 27.
Zaur Dadayev and Anzor Gubashev are of Chechen origin.
Three other suspects were remanded in custody. A sixth man is reported to have killed himself in a standoff with police in the Chechen capital Grozny.
The suspect threw one grenade at the arresting officers and blew himself up with another, a security source told Interfax news agency.
Boris Nemtsov, a former deputy prime minister and veteran liberal politician, who was 55, was shot in the back four times as he was walking with his girlfriend within sight of the Kremlin. He was buried in Moscow on March 3.
Anzor Gubashev and Zaur Dadayev, who are both accused of organizing and carrying out the murder, were brought into court amid heavy security.
Chechen leader Ramzan Kadyrov said Zaur Dedayev was a devout Muslim who was shocked by cartoons of the Prophet Muhammad published by the French satirical magazine Charlie Hebdo.
Russian investigators have previously said they were looking into the possibility that Boris Nemtsov was killed over his defense of Charlie Hebdo.
In a statement on his Instagram account, Ramazan Kadyrov also confirmed Zaur Dadayev had been a member of the Chechen police who was decorated for his bravery.
The other suspects include Anzor Gubashev’s younger brother Shagid Gubashev and two men named as Ramzan Bakhayev and Tamerlan Eskerkhanov. Reports say all three have denied any involvement in the murder.
Four of the men come from the northern Caucasus region and were detained in the republic of Ingushetia which borders Chechnya, Russian media say.
The Russian Investigations Committee is treating the case as a “contract killing”, Interfax news agency reported.
According to the sections of the criminal code cited in court, investigators believe the murder was carried out by a group of people, that it was committed on contract for financial gains, and that it also involved extortion and banditry, Interfax says.
President Vladimir Putin has condemned Boris Nemtsov’s murder and called for an end to “shameful” political killings in Russia.
However, leading opposition figure Alexei Navalny accused the Kremlin of ordering the assassination to cow the opposition amid Russia’s mounting economic problems.
Boris Nemtsov was killed just days before a march against the war in Ukraine that he was organizing.
Boris Nemtsov had also been drafting a report expected to expose covert Russian military involvement in the conflict.