Russian ex-spy Sergei Skripal and his daughter Yulia were poisoned in March.
The group said it identified Mishkin through passport information, residents' databases, auto registration records and phone records, as well as personal testimony from people who know him.
Boshirov has been unmasked as decorated Russian agent Anatoliy Chepiga while Petrov has been identified as trained army doctor Alexander Mishkin.
Russian presidential spokesman Dmitry Peskov said: "I already told you last week that we won't continue any discussions on (reports) of media channels and various civil research organisations".
The names on the pair's travel documents were Ruslan Boshirov (on the left above) and Alexander Petrov (on the right).
British officials said when they charged two Russians last month in the March nerve agent attack on Sergei Skripal and his daughter that they believed Petrov was an assumed name.
He was recruited by the secretive GRU, given the undercover identity of Alexander Petrov when he was stationed in Moscow and made multiple trips to Ukraine, the investigative group said.
The grandmother of the military doctor outed as a Salisbury assassin has disappeared after disclosing her grandson had been awarded Russia's highest honour by Vladimir Putin.
But Mishkin's cover identity had retained key details from his real identity, including his date of birth, as well as his first name and patronymic - a middle name based on a person's father's name, a practice that is common among Russians.
The second suspect in the attempted poisoning of a former Russian secret agent has been identified by an investigative website.
He moved to St Petersburg and enrolled at the S Kirov Military Medical Academy, specialising in undersea and hypobaric medicine for the Russian navy and graduating as a senior lieutenant.
"We shouldn't also forget that there was a big effort made by our police and MI5 to spot them in the first place, track their movements and also. the huge effort that went in to develop the intelligence that helped guide us to the door of the GRU itself".
The Kremlin said it had been unable to find any record that Chepiga had been awarded the Hero of the Russian Federation decoration, despite it being referenced on Chepiga's military academy's website and engraved in gold on an honors wall there.
At Loyga a reporter with the Insider "was able to meet and talk to many residents who all recognised "Alexander Petrov"... as "our local boy" Alexander Mishkin", the Bellingcat report said.
The U.S. Justice Department also charged seven GRU officers in an alleged worldwide hacking rampage that targeted more than 250 athletes, a Pennsylvania-based nuclear energy company, a Swiss chemical laboratory and the chemical weapons watchdog. Nor has the Kremlin been helped by other GRU agents in recent Russian espionage operations in Europe, who appeared also weak on the basics of traditional spycraft.
Russia's foreign minister Sergey Lavrov has dismissed the allegations, saying the men who were expelled from Holland had been there on a "routine" assignment to provide cybersecurity support for Russia's embassy.