The announcement, made in a statement on Wednesday, is the first time the EU has awarded its "Protected Geographical Indication" status to a Cambodian product.
The ruling means only pepper grown in the southern Cambodian province under specific conditions can market itself inside EU member countries as Kampot pepper.
"Mrech Kampot (Kampot pepper) will benefit from a very high level of protection on the EU market," the EU said in a statement.
Kampot has long been regarded by many chefs as producing one of the world's finest pepper strains. The peppercorns come in green, white, black and red varieties, with the latter the most sought after.
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It gained global acclaim during the French colonial occupation of Cambodia when it was exported widely, but the industry was nearly wiped out during the Khmer Rouge era.
In more recent years it has bounced back, with Kampot pepper gracing hip restaurant menus across the globe.
Nguon Lay, president of Cambodia's Kampot Pepper Promotion Association, said he was grateful for the new protection that would prevent marketers from slapping the name onto products which were not authentic.
Although most of the EU's protected foods are produced inside member states, it has increasingly awarded the status further afield.
Some 20 non-EU products now have protected status, including Turkey's Gazientep baklava pastries and India's Darjeeling tea.