Raed Jaser, 35, of Toronto and Chiheb Esseghaier, 30, of Montreal who face charges of conspiring "with each other to murder unknown persons for the benefit of, at the direction of, or in association with a terrorist group," denied the allegations made against them yesterday.
They were arrested on Monday in separate raids after what police said was a joint Canada-US investigation that started in August last year after a tip from a member of the Muslim community.
Police confirmed the plot and said it involved a passenger train route in the Toronto area, and that there had been no immediate threat to rail passengers or to the public.
The US Federal Bureau of Investigation was also involved in the investigation.
The arrests came a week after the Boston Marathon bombings that killed three people and wounded 200.