Recep Tayyip Ergodan considers the YPG to be a part of the PKK, a Kurdish separatist group that both Turkey and the U.S. consider to be a terrorist organization.
Bolton warned Syria's president, Bashar al-Assad, not to use the USA drawdown as a pretext to use chemical weapons against Syrians, saying there is "no change" to the US position that their use is a "red line".
Ibrahim Kalın, a spokesman for Turkish President Recep Tayyip Erdogan, said following Bolton's remarks that any allegation that Turkey is targeting Kurds is "irrational". "That's what the president said, the ones that fought with us".
That's signaling a pause to a withdrawal abruptly announced last month and initially expected to be completed within weeks. Ankara regards the YPG an extension of the PKK, a Kurdish armed group that has waged an insurgency in southeast Turkey for over three decades. PKK is the outlawed Kurdistan Workers' Party.
Bolton had said the protection of USA allies in Syria, including the YPG, was among "the objectives that we want to accomplish that condition the withdrawal" of USA forces.
Bolton's comments were the first public confirmation that the drawdown has been slowed. Trump had faced widespread criticism from allies about his decision, including that he was abandoning the Kurds in the face of Turkish threats.
They are from dozens of different nationalities and include a significant contingent from France, the main United States partner in the coalition assisting Kurdish forces.
The United States of America leaves some of the forces in southern Syria for an unknown period of time after withdrawal of the main troops, reports NBC with the reference to its sources in the Pentagon.
John Bolton said there is no timetable for the pullout, but insisted the military presence is not an unlimited commitment.
Turkey wants the U.S.to provide air support for its troops against Islamic State militants who hold several villages near the Syria-Iraq border and the city of Hajin, which lies more than 250 kilometers (155 miles) south of the Turkish border, said the person, who has direct knowledge of Turkey's plans but isn't authorized to speak to the media. Bolton acknowledged that pockets of ISIS remain. Turkey hates ISIS maybe not as much as we do. The U.S. has an estimated 2,000 troops in Syria, mostly in the northeast. The YPG withdrew from Manbij last Wednesday as part of a deal with President Bashar al-Assad's government, the official Syrian Arab News Agency reported.
But he said Mr Trump's position was Turkey may not kill the Kurds and that the U.S. withdrawal would not take place without an agreement on that.