The FBI "is investigating the Russian government's efforts to interfere in the 2016 presidential election", Comey told a hearing by the House Intelligence Committee.
"And that includes investigating the nature of any links between individuals associated with the Trump campaign and the Russian government and whether there was any co-ordination between the campaign and Russia's efforts," he said.
Comey's disclosure confirmed longstanding reports that the Federal Bureau of Investigation was probing the explosive charges that Trump's stunning election victory over Hillary Clinton last November came on the back of Russian meddling.
US intelligence chiefs said in January they were convinced that Russian President Vladimir Putin was behind that effort.
But they had not commented on whether they were examining links between members of Trump's campaign and Russian officials.
Republican committee chair Devin Nunes opened Monday's hearing - the first public hearing into the issue - by saying the panel had "seen no evidence to date that officials from any campaign conspired with Russian agents".
But Adam Schiff, the Democratic vice chair of the committee, detailed a list of alleged links and communications between the Trump team and Russia.
"Is it possible that all of these events and reports are completely unrelated, and nothing more than an entirely unhappy coincidence? Yes, it is possible," he said.
"But it is also possible, maybe more than possible, that they are not coincidental, not disconnected and not unrelated, and that the Russians used the same techniques to corrupt US persons that they have employed in Europe and elsewhere."