While no cases of Ebola have been reported anywhere near North Korea, the country shut out foreign tourists in October with some of the strictest Ebola regulations in the world.
North Korean media have suggested Ebola was created by the US military as a biological weapon.
Nick Bonner, co-founder of Beijing-based Koryo Tours, said he did not think the decision reflected any deeper problems in the North's secretive and often enigmatic government, though the news comes amid reports leader Kim Jong Un has called for increased combat readiness and, at a meeting of senior party and military leaders, described tensions on the peninsula as graver than ever before.
Joint military exercises between the US and South Korea that the North says are a provocation will also begin soon.
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Bonner said more than 400 foreign runners had signed up with his agency alone for the event, which is to be held April 12.
He said he was informed by officials on Monday that the race billed as one of the most exotic marathon locales on Earth would be open only to local runners.
Bonner, speaking with The Associated Press by phone from Beijing, said he remains hopeful the Ebola restrictions will be lifted by the end of March. Even if they are, however, the restrictions apparently made it too difficult for marathon organizers to be ready in time to deal with the influx of foreign runners.
Last year's race through the streets of Pyongyang, including a 10-kilometer (6-mile) competition and a half marathon along with the full course, was opened up to foreign recreational runners for the first time and was a big success.
Known officially as the Mangyongdae Prize International Marathon, the race is sanctioned as a bronze-label event by the International Association of Athletics Federations and has been held annually for 27 years.
It is held in conjunction with a series of sporting competitions, arts festivals and cultural events marking the birthday of North Korea's founder, Kim Il Sung, on April 15.