And in the political crosshairs are several US citizens -- as well as Turks working for American diplomatic missions -- detained in an ongoing purge that followed a failed military coup last year.
The Turkish government accuses many of them for having links to the Turkish Muslim cleric Fethullah Gulen, who lives in exile in the US and whom Turkey blames for orchestrating the failed coup. Ankara considers Gulen and his followers terrorists, and so has made terror allegations against many of the American detainees.
Up high on the Turkish government's list of grievances is the US' refusal to extradite Gulen. Another is Washington's continued support for Kurdish factions fighting ISIS in Syria -- Ankara considers them terrorists who threaten Turkey's sovereignty and security. The US supports and arms them
, and considers them a reliable force fighting ISIS.
One cleric for another
Among the US citizens detained is American pastor Andrew Brunson, who was arrested a year ago in Izmir, where he lived and worked at a church.
Brunson was told that he was detained for being a "national security risk" and was later charged with having links to a movement inspired by Gulen.
Gulen lives in exile in Pennsylvania, and Ankara has repeatedly pressured Washington to extradite him. The US has said that it does not have enough evidence to legally do so.
Nearly two weeks ago, Erdogan, who sees Gulen as his nemesis, made it clear in a televised speech that Ankara could swap Brunson for Gulen.
"'Give us the pastor back', they say. Well, you have a pastor as well. Give that one back to us, then we will give him (Brunson) back to you," Erdogan said.
Fadi Hakura, who manages the Turkey Project at Chatham House in London, said the remarks had "raised question marks" in Washington.
"It has created the perception in Washington that Brunson was illegally arrested as a bargaining chip."
Clyde Forsberg, an American academic, told CNN that he was detained in the town of Karabuk for four days the month after the failed coup.
He mused that instead of Brunson "it could easily have been me."
Forsberg was fired from his job and arrested after he wrote and posted poems on Facebook about his colleagues who had been detained in the purge. He was charged with aiding and abetting a terrorist organization, he said.
"The interrogations were so absurd. They asked questions like, do I have books? I'm a university professor. What they meant to ask was do I have Gulen books? I worked out that the answers to everything had to be no," he said.
The Turkish Foreign Ministry did not immediately respond to CNN's request for comment.
Lives in disarray
Another American detained is Serkan Golge, a 37-year-old NASA physicist who holds dual Turkish-US citizenship.
He was working on a project to send astronauts to Mars, looking at the effects of space radiation on astronauts.
He was on holiday in Turkey when he was arrested, accused of having links to the Gulenist movement.
Golge's wife, Kubra Golge, dismissed the allegations as ridiculous and said the 14 months without her husband had been "the most painful in my life."
"My entire body aches but I'm not sick. Or it feels like someone has smashed a hammer through my head and just left our lives in complete disarray," she told CNN.
"I hope this all works out. Sometimes I have hope and other times I have none. I cannot see the future."
The couple have two children and have had to put their home in Houston up for sale, she said. Her husband is now on unpaid leave and the pair have been unable to keep up their payments.
Their 7-year-old son is now attending school in Turkey.
"But he has trouble adjusting. He keeps dreaming of going back to the US."
But Gulen is not the only contentious issue. Turkey has also feuded with the US over its support for Kurdish fighters in Syria.
The US has backed an alliance of rebel fighters -- the Syrian Democratic Forces -- in its effort to eradicate ISIS from the country. The problem is that the backbone of the alliance is the Kurdish People's Protection Units (YPG), a Syrian offshoot of the Kurdistan Workers' Party (PKK).
Turkey and the US both consider the PKK a terrorist organization, but they differ on their stance when it comes to the YPG.
The US sees the Kurdish fighters in Syria as the most crucial and reliable of local forces in Syria, while Turkey is concerned that the Kurds could gain territory in Syria on Turkey's southern border.
One person who has been detained over links to the PKK is Hamza Ulucay, who worked for more than three decades in the US mission in Adana.
He is not a US citizen, but he was the first of two Turkish nationals working for the US mission to Turkey who have been arrested this year. The second, whom state media named as Metin Topuz, was detained in September and formally arrested last week for having alleged links to Gulen as well as for espionage. It was his arrest that kicked off the visa row.
A third consular staff member is now being sought by prosecutors
, who have already detained and charged his wife and adult child.