During the Civil War, the St. Peter and Paul Fortress was one of the places where the Bolsheviks shot the convicts - White Guards, counter-revolutionaries, class enemies and anyone who could be detained "by mistake". The mass graves of the victims of the Red Terror, who were buried here, on Zayachiy Island, have not been touched for eighty years and only relatively recently in 2010, archaeologists have taken up excavations on the territory of the fortress. Under the guidance of archaeologist Vladimir Kildyushevskiy, a researcher at the Institute of the History of Material Culture of the Russian Academy of Sciences, excavations are underway here of the burial places of victims of the Red Terror, who were shot in 1918-1919. People were piled on top of each other in seven tiers. They were simply thrown off at random, the graves were dug relatively shallow only 1.2-1.3 meters. Naturally, when there are two or three bullet holes in the skull, or if the head is pierced with a butt or a bayonet, it is obvious that these are not people who died a natural death.
"For the most part, they are young, from 20 to 45 years old, - Vladimir Kildyushevskiy, through the window of a small office, points to the shore of the Kronverk Strait, - there, along the Golovkin Bastion, the main burials were found."
The Red Terror was declared on September 5, 1918 by the Decree of the Council of People's Commissars of the RSFSR. Officially, it was stopped after two months, but many historians attribute all the repressions that the Bolsheviks carried out during the Civil War to the Red Terror. According to the official data of the Cheka, about 800 people were shot in Petrograd at that time, according to historians about 1200. One of the places in Petrograd where convicts were shot was the prison of the St. Peter and Paul Fortress, which had been in the Trubetskoy Bastion since 1872. In January 1919, four Grand Dukes of the Romanov dynasty were executed in the fortress: Georgiy Mikhaylovich, Dmitriy Konstantinovich, Nikolay Mikhaylovich and Pavel Aleksandrovich, but the exact place of their burial is unknown. The prison ceased to exist in the early 1920s.
The fact that human remains were buried near the walls of Petropavlovka was known before. Until the 1950s, the St. Peter and Paul Fortress belonged to the military department and the mint, and the territory along the Golovkin Bastion, facing the Kronverk Strait, was built up with sheds, technical rooms and other buildings that arose in the Soviet era. In 1954, the fortress was transferred to the State Museum of History in St. Petersburg, which undertook the improvement of the territory, after which the unnecessary buildings were demolished, while digging up part of the land. "During the work, bones were repeatedly found here. People who lived here as children told us about this. They said that the guys ran around the territory of the fortress, along the beach and stumbled upon bones. Well, they say, we handed them over to scrap for bone meal. And we were buying ice cream on money we received. Of course, no research was carried out at that time," says Kildyushevskiy. - The prison in the Trubetskoy Bastion was considered a liquidation prison, that is, people who were sentenced to death were brought there. Judging by the documents that we managed to find, 15, 20, 25 people were sentenced at once and they were shot. And since this territory was closed it was fenced with a high fence and they dug out a mass grave and buried the executed people.

The identification of the remains of Major General Aleksander Nikolayevich Rykov, the hero of the defense of Port Arthur, is one of the main victories of archaeologists. As Kildyushevskiy says, this discovery was accompanied by a "chain of happy accidents."
The mass grave where Rykov lay was excavated in 2009. Scientists immediately noticed that a disabled person without one leg was buried there. Then they found in the archives the "case of Kovalevskiy", about the execution of members of the counter-revolutionary organization of the military doctor Vladimir Pavlovich Kovalevskiy, among whom there was also one disabled person. Archaeologists managed to find the descendants of Rykov - his grandchildren even kept a note that the Major General wrote from St. Peter and Paul Fortress. To confirm the relationship, Rykov's relatives decided to conduct a genetic examination at their own expense, however, as it turned out, this requires a direct descendant of a person, while the daughter of the executed military commander died back in 2000.
- When they began to think that maybe it was necessary to do an exhumation and so on, the geneticist asked if there was some thing that belonged to her and from which DNA could be taken - hair or something else. The grandchildren said, here, we have letters that she wrote and sealed. DNA was isolated from this glue, from saliva. When compared with the father, with the grandchildren, a whole chain lined up. This is the only such case and the geneticist was jumping for joy that they managed to establish kinship, - says Kildyushevskiy. - Of course, this is a very expensive examination. It still needs high-quality drugs, which are not available in Russia.
Source - https://paperpaper.ru/krasniy-terror/