Anastasiya Baburova, a 25-year-old trainee reporter on the opposition newspaper Novaya Gazeta, was also shot as she left the media briefing with Markelov. She later died of her injuries in hospital.
Markelov acted for the family of an 18-year-old Chechen girl, Elza Kungayeva, whose murder in 2000 came to symbolise human-rights abuses in Chechnya.
Colonel Yury Budanov, who was convicted of strangling Kungayeva, was released from jail on Friday after serving just over half of a 10-year sentence for her murder.
Budanov's release sparked a series of protests in Chechnya and Markelov had vowed to fight the reduction of the colonel's sentence.
Elza's father, Visa Kungayev, said he was "shocked" by the killing and told Echo of Moscow radio that Markelov had recently been on the end of death threats because of his involvement in the case.
Human-rights activists were quick to condemn the killing, with Tanya Lokshina, deputy head of Human Rights Watch in Moscow, describing it as "outrageous".
Lokshina said the shooting was comparable to the 2006 murder of Anna Politkovskya, a journalist who reported on human-rights abuse in Chechnya.
"This is a country in which murders of those defending human rights are now becoming everday routine"
Karina Moskalenko, Russian human rights lawyer
Karina Moskalenko, a lawyer for relatives of Politkovskya, said: "It is terrible that this has become a grim reality of our life ... this is a country in which murders of those defending human rights are now becoming everyday routine."
Markelov had also provided Politkovskya with legal advice and Baburova was an intern on the newspaper the veteran journalist reported for.
Human rights organisation Amnesty International has urged the Russian authorities to investigate the killing "promptly, fully and objectively".
"Markelov's murder is a despicable crime," Nicola Duckworth, Amnesty's Europe and Central Asia programme director, said.
"Silencing those who defend human rights and work to uphold the rule of law is absolutely unacceptable."
Yuri Chaika, Russia's prosecutor-general, said he had taken the investigation into Markelov's murder under his personal control.
Russia has fought two full-scale wars in the predominantly Muslim Chechnya since the collapse of the Soviet Union in 1991.
While large-scale hostilities have ended in the southern region, low-level skirmishes between Chechen and Russian forces are reported to still occur on a regular basis.