Koki Manunga and Joyce Zakary "have accepted provisional suspensions following positive samples provided in Beijing on the 20th and 21st of August respectively", the IAAF said in a statement.
Track and field's world governing body said the Kenyan pair had been tested at the athletes' hotel before their competition started as part of "targeted tests".
Zakary clocked a national record of 50.71 seconds in Monday's first round of the women's 400m at the Bird's Nest, but did not start the semi-final yesterday for which she had qualified.
Kenya was rocked this year when marathon star Rita Jeptoo was banned for two years after being caught doping with the banned blood-boosting hormone EPO.
Jeptoo is the biggest name in Kenyan sports ever to have been caught, and the bust has been a major trauma for a country that idolises its medal-winning and record-breaking runners.
Top Kenyan athletes earlier this month called for the national governing body, the International Association of Athletics Federation (IAAF) and the world's anti-doping body WADA to take action over reports of widespread doping.
ARD alleged doping was ongoing in Kenya, and claimed there was "massive corruption" within the Kenyan set-up and "a desire to cover-up doping... To the summit of the Kenyan athletics federation".
Athletics Kenya, the nation's governing body, said it had "watched with grave concern the German TV ARD documentary", calling the broadcast, which coincided with the national trials for the world championships in Beijing, "extremely suspect and ill motivated".
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