The two, both residents of the North Caucasus Republic of Ingushetia, were detained in the town of Nazran on Tuesday. Their names have not been disclosed.
"One of the suspects was released after a probe, and the other was transferred from Ingushetia for further investigation, as there are grounds to suspect him of involvement in the Nevsky Express explosion," the source said over the phone.
The Nevsky Express hurtled off the rails near Veliky Novgorod on August 13 on the country's busiest rail line, linking Moscow and St. Petersburg, following an explosion that left a crater in the tracks. Carriages were overturned and dozens of people were injured.
The blast occurred as the train was approaching a railway bridge over a road, but the train, traveling at around 190 kilometers per hour (118 mph), had sufficient momentum to make it over the bridge before running into the embankment, avoiding potentially massive fatalities.
A total of five suspects were earlier detained in the case, several of them were later released on the condition that they report to police on a regular basis.