After arriving at Havana airport yesterday, Trudeau headed straight to the city's iconic Revolution Square and laid a wreath, an AFP photographer saw.
He was scheduled later to meet with Cuba's President Raul Castro, officials said.
The two-day visit is the first stop on a tour that will also take Trudeau to Argentina and to Peru for the APEC Asia-Pacific trade summit.
It comes 40 years after Trudeau's father Pierre Elliott Trudeau committed to a lifelong friendship with Cuba's former revolutionary president Fidel Castro during a similar visit.
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The visit will also provide an opportunity to "collaborate more closely on sustainable economic growth, inclusive governance, security, climate change, and gender equality," a statement said.
Trump, who won the US presidential election a week ago, has sent mixed messages about the thaw in US-Cuba relations which was started two years ago by current US President Barack Obama.
Trump gave it a lukewarm welcome at first, before vowing to reverse the new policies unless Raul Castro agrees to democratic reforms and other demands.
Because Obama used executive authority to enact the rapprochement, Trump could change course just as easily to reinstate financial, trade and travel restrictions.
The visit is primarily "symbolic," John Kirk, a politics professor and Cuba expert at Dalhousie University in Halifax, told AFP.
Ottawa also remained steadfastly opposed to the American trade embargo on Cuba, which has not been revoked by Congress.
Officially, no meeting is planned with Fidel Castro, but "there's a chance" they will see each other, Cuba's ambassador to Canada, Julio Garmendia Pena, told Canadian media.
The visit is the first by a Canadian leader to Cuba since Jean Chretien in 1998.
Yet it was also Harper who hosted secret talks between US and Cuban officials in 2014 leading to the rapprochement.
Today, Cuba continues to welcome a huge influx of Canadian tourists each year -- 1.3 million or nearly 40 percent of all tourist visitors.
Bilateral trade remains modest at less than $1.0 billion annually.
Despite their warm diplomatic ties, many Canadian companies do not invest in Cuba over fear they will be blocked from the US market.