The two countries, which every year kill tens of thousands of seals, insist that the hunting method is ethical and asked the WTO to review the 2010 ban, imposed because of what the EU considers cruel hunting methods.
Canada's indigenous Inuits, who have traditionally hunted seal for centuries, are exempt from the ban.
Commercial seal hunters often use a hakapik, a club with a metal spike on it, to stun the seals before killing them. Animal rights groups also say some seals are skinned while they are still conscious.
Canada, home to some 6 000 commercial seal hunters, argued on Monday that stricter regulations have made the hunt more humane.
"East Coast seal hunt can be, and is, conducted in a humane fashion," Canada's representative said by video link to the hearing in Geneva.
The WTO, which will also hear Norway and the EU in the case, is expected to deliver a decision in a few months.
Ahead of Monday's hearing, the animal rights group Peta staged a protest outside the WTO headquarters.