The Prime Ministerâ€™s Office said Trudeau reaffirmed Canadaâ€™s solidarity with the people of Orlando, families and friends of the victims and the LGBTQ community.
He and Obama agreed on the importance of fighting hate and intolerance, and the need to promote and protect pluralism and diversity.
Obama said he was grateful to the people of Canada for their support.
He also expressed condolences for the killing of Robert Hall by the Abu Sayyaf terrorist group in the Philippines.
The two men said they will continue working together in the fight against terrorism.
On Tuesday evening, Trudeau paid a visit to the U.S. Embassy in Ottawa to pay his condolences for the victims of the Orlando shooting.
Once inside the ambassadorâ€™s office, Trudeau sat at a glass-topped table and leafed slowly through a book of condolence with Sophie Gregoire Trudeau standing to his right and U.S. Ambassador Bruce Heyman seated to his left.
â€œBeing friends is about celebrating in the good times, but even more about being able to lean on each other during the toughest times. Des grands amis, toujours,â€ Trudeau wrote in the book.