The prosecutors told the jury that experts had determined that threads found on the weapon came from the upholstery of the car used by Rustam Makhmudov, the man suspected of pulling the trigger, and at least one of his brothers.
The formal owner of the car, Makhmudov' cousin, earlier said he had given the car to Rustam, Rustam Makhmudov remains at large.
Prosecutors also showed footage from a surveillance camera showing the car on the street near Politkovskaya's Moscow apartment several days before she was killed, and also on October 7, 2006, the day of her murder.
Politkovskaya, known for her criticism of the Kremlin and reports of military atrocities against civilians in the troubled Chechen Republic, was gunned down in an elevator in her Moscow apartment in what police described as a contract killing.
Three men are currently on trial on charges of involvement in the murder; a former police officer and two other Makhmudov brothers, Dzhabrail and Ibragim, all residents of Chechnya.