The Russian Prosecutor General’s office announced plans to challenge the verdict.

According to the Committee to Protect Journalists, 16 journalists have been killed in Russia because of their work since 2000. The most recent was Anastasia Baburova, who was shot Jan. 19 along with the lawyer Stanislav Markelov as they left a news conference. Only one of those 16 cases has resulted in a conviction, and none of those who organized the killings have been found.

“Russia is a country where for years and years now, journalists who cover human rights issues and corruption are being murdered and assaulted,” said Miklos Haraszti, the Organization for Security and Cooperation in Europe’s representative for media freedom.

Image Dzhabrail Makhmudov, left, and his brother Ibragim, right, with their lawyer, Murad Musayev. Credit... Misha Japaridze/Associated Press

“It has to be admitted, at the highest level of the country, that there can be no free speech in a country where the best journalists are afraid for their lives for doing their jobs.”

The three-month trial took place in a cramped courtroom, where the murder suspects watched from behind the bars of an iron cage. Two were brothers, Ibragim and Dzhabrail Makhmudov, who prosecutors said had assisted their brother Rustam in stalking Ms. Politkovskaya to her apartment. Rustam, who prosecutors say was the gunman, is believed to be in hiding.

A third murder suspect, Sergei Khadzhikurbanov, was accused of having hired the Makhmudov brothers, provided the weapon and coordinated the murder. A fourth defendant, Col. Pavel A. Ryaguzov, was accused of criminal ties to the killers, but no role in the killing itself. He was also acquitted Thursday.

The prosecution offered thin evidence, relying heavily on cellphone billing records that showed that the suspects called one another from areas around the crime scene before and after the murder took place. The jury deliberated for two hours before returning its verdict.