Among those requested to leave are the families of American soldiers at the Incirlik air base. The US State Department and Pentagon cited continued security fears for the notice.
Among those targeted for evacuation were dependents of employees at the US consulate in Adana, in south-central Anatolia province.
Others include relatives of US service personnel, based at the Incirlik air base, close to Adana, where the US Air Force maintains a roughly 5,000 strong military presence. Families of staffers based in Ismir and Mugla provinces must also leave southern Turkey.
In a statement, the military's European Command, based in Stuttgart, Germany, said the "ordered departure" notice "allows for the deliberate, safe return of family members from these areas due to continued security concerns in the region."
"We understand this is disruptive to our military families, but we must keep them safe and ensure the combat effectiveness of our forces to support our strong ally Turkey in the fight against terrorism," said EUCOM commander General Philip M Breedlove.
Fears of new attacks
The order to leave follows four bomb attacks in the Turkish cities of Ankara and Istanbul in recent months, which have left more than a hundred people dead. The blasts have been blamed on IS.
It comes after Israel on Monday urged its citizens to leave Turkey and advised Israeli tourists to postpone any planned trips for fear of an imminent attack on Jewish interests.
The Pentagon said the order would affect about 680 family members, including children, while the State Department did not give figures.
Both US agencies had begun a voluntary drawdown of staff at the two posts last September after Turkey announced it would take a greater role in the fight against IS.
At the time, military officials warned of specific calls by militants for lone wolf attacks against the air base.
The Incirlik air base is being used to support US-led coalition airstrikes against the "Islamic State" (IS) militant group in Syria and Iraq. Washington has deployed F-16 fighter jets to the base.
Turkish President Recep Tayyip Erdogan is due in the US this week to attend President Barack Obama's nuclear security conference.