This is a developing story and may be updated.
At least 20 others were also injured in the blast.
Information thus far indicates the cause was an "unidentified explosive device," Andrei Przhezdomsky, spokesman for the National Anti-terrorist Committee, said to Rossiya-24 TV.
Twitter user @QuerdenkerLE 2h posted this video which shows the subway train car doors partially blown off:
— Sachse & Kosake (@QuerdenkerLE) April 3, 2017
The explosion led to the closure of several metro stations as well tightened security at the St. Petersburg airport, Pulkova.
An attack on St Petersburg, Russia's old imperial capital, would have some symbolic force for any militant group, especially Islamic State or Chechen secessionist rebels. Attacks in the past have largely concentrated on Moscow, including an attack on an airport, a theater, and in 2010 a metro train.
St. Petersburg-native Russian President Vladimir Putin was in the port city Monday for a meeting with Belarusian President Alexander Lukashenko.
"The reasons for the explosion are unknown, so it's too early to talk about it. The investigation will show what happened," Putin said at the start of his meeting with Lukashenko, CNN reports. "Naturally, we always consider all options—both domestic and criminal, primarily incidents of a terrorist nature."
The Kremlin promised a "full investigation" into the explosion.
Twitter users were tracking developments with the hashtags #StPetersburg and #StPetersburgBlast: