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Quarantine officers destroyed 15,000 chickens, ducks and turkeys in farms and restaurants across the capital.
The cull began just hours after the authorities recorded Seoul's second outbreak of the virus in a week.
Bird flu has caused 240 deaths globally since 1993. Tests are being carried out to determine if the South Korean outbreak was the deadly H5N1 strain.
The virus was detected in southern parts of the country last month forcing the slaughter of nearly seven million birds.
The government is now concentrating on preventing live poultry from being brought into Seoul.
Two outbreaks of the virus have also been reported on farms in Busan and Ansung. It is the first time the virus has been found in Busan - South Korea's second largest city.
Agriculture Ministry spokesman Yoon Young-ku said the outbreaks brought the number of confirmed detections of the virus in South Korea to 28.
Bird flu is currently relatively difficult for humans to catch, but health authorities fear it could mutate into a form that is much more easily spread among humans, which could cause a pandemic.
The World Health Organization says at least 240 people have died from bird flu since 2003. Most human cases so far have been linked to direct contact with infected poultry.
(BBC)
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