The long-running tuna trade feud between the North American neighbours centres on the controversial "dolphin safe" label.
For more than two decades the United States has required all tuna imports to be certified "dolphin safe", part of a campaign to save a species that had been decimated by fishing nets.
But Mexico argues that the US applies stricter standards to its exporters to acquire the "dolphin safe" certification than to those from other countries.
The Geneva-based WTO, which aims to ensure a level playing field in global trade, cannot force countries to change their trade policies.
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But it can authorise retaliatory measures against countries that do not comply with its rulings.
Today's decision follows the US refusal to adjust its labelling of Mexican tuna.
A WTO arbitrator authorised Mexico to hit US exports with USD 163 million (149 million euros) in annual tariffs in response.
But the dispute looks set to carry on.
Last year, Washington amended its tuna labelling guidelines, applying the tougher standards applied to Mexico to all importers.