Thursday's case, in a different part of the city, was the capital's first in nearly two months.
The coronavirus is believed by many to have emerged at a seafood market in Wuhan, the capital of Hubei province, in December.
Both the newly infected men, aged 25 and 37, had had no contact with people from Hubei or travellers from overseas in the last 14 days, state media said, though the younger man was briefly in Qingdao city in the eastern province of Shandong.
The research facility where the men worked, the China Meat Food Comprehensive Research Centre, in Fengtai district in the south of Beijing, remained open on Friday, according to the state-run Beijing Daily.
Reuters could not immediately reach the Beijing Academy of Food Sciences, which oversees the centre, for comment.
State-controlled Beijing News said six wholesale food markets in the city recently visited by the two men had been either wholly or partially shut.
City authorities had shut beef and mutton trading at the Xinfadi wholesale market, while the Jingshen seafood market had entirely closed. Both markets lie within a 7 km radius of the meat research facility.
The Beijing city government said it had dropped plans to reopen school on Monday for students from the first to third grades because of the new cases.
It also said restaurants would be inspected and checks made on seafood products and fresh and frozen meats.
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