The detainee, Saleh Aruri, was taken from his home before dawn, his wife said.
Aruri was described on a Hamas Web site as the founder of Iz a Din al-Kassam, its West Bank military wing.
Aruri had served 15 years in an Israeli prison and was released in March, the Web site said.
Hamas alleged in a statement that its political rival, the Fatah movement of Palestinian Authority Chairman Mahmoud Abbas, is coordinating with Israel in an attempt to crush Hamas in the West Bank.
IDF officials said Aruri resumed involvement in violent Hamas activity in recent months.
Earlier on Friday IDF soldiers shot and killed a Palestinian man at a West Bank roadblock near the city of Hebron.
The man was later identified as Shadi Matoor, 25.
The IDF said Matoor had tried to enter a military outpost north of Kiryat Arba. When he did not respond to soldiers' calls to stop, the troops shot at him, the army said.
According to a preliminary investigation, Matoor was unarmed.
The man was seriously wounded and taken to a hospital in Hebron, where he later died of his wounds.
Sources in the IDF maintain that Matoor was wearing IDF army pants and high boots, and soldiers suspected he was attempting to infiltrate to the outpost.
Security forces nab 'Hezbollah-trained' suspect in W. Bank raid
IDF and Border Police troops early Friday morning arrested three suspected militants in an overnight raid in the West Bank city of Nablus.
Security forces said one of the suspects, Yusuf Abu Layla, is a senior member of the Fatah-affiliated Tanzim who had received training and instructions from Hezbollah to carry out terror attacks in Israel.
The two other suspects are Moeib Hoteri, also of Tanzim, and Yusuf Mabruk, a member of the Popular Front for the Liberation of Palestine.
During the operation, soldiers opened fire on a car with five suspects that fled the scene, wounding one of the passengers. The wounded man and another suspect escaped, while the three others barricaded themselves in a building.
Troops surrounded the structure and called on them to surrender. They were caught while trying to escape. No IDF soldiers were hurt in the firefight.
Abu layla is an explosives device expert who planned bombings in Israel, the army said. In addition, it claimed he was involved in manufacturing suicide belts for Tanzim in Nablus, as well as training others how to make bombs.