Anadolu news agency said Salih Muslim, former co-chair of the Democratic Union Party, or PYD, was detained on Saturday in Prague.
Muslim features on a Turkish interior ministry wanted list, with a 4 million lira (860,000 euro) bounty for his arrest.
A further red notice was issued on February 13, which included Muslim on the most wanted list and offered a 4-million-Turkish-lira (1.05 million US dollars) bounty for him.
Turkey considers the PYD in Syria and its armed wing, the Kurdish People's Protection Units (YPG), to be "terrorist groups" with ties to the banned Kurdistan Workers' Party (PKK).
Muslim stepped down as its co-chair a year ago but remains influential.
It said he was due to appear in a Czech court and that the Turkish authorities would press for his extradition. The decision to detain him was made on February 24 by the Interpol's office in the Czech Republic on the basis of Ankara's request.More news: Afghan Govt. to shut down Taliban Doha office
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Ankara last month launched a military operation against the YPG militia in the enclave of Afrin in northern Syria.
At the beginning of the Syrian conflict in 2011, Turkey wanted to negotiate with Syrian Kurds and met with Muslim several times in Ankara.
"They will go back to Afrin to live in peace after Inshallah (God willing) PKK, PYD, YPG, and Da'esh are cleared", Yildirim said, according to state media.
The Turkish Army has invaded the Afrin region in Northern Syria, in an attempt to capture Kurdish-held areas.
On Saturday, Muslim tweeted images of children he claimed to be killed in Turkey's military operation in Syria, accusing Erdogan of being a "child killer".
The United States and European nations regard Syrian Kurds as important partners in the fight against Islamic State militants and other extremists.