ANTAKYA, Turkey — A Pentagon program to train moderate Syrian insurgents to fight the Islamic State has been vexed by problems of recruitment, screening, dismissals and desertions that have left only a tiny band of fighters ready to do battle.

Those fighters — 54 in all — suffered perhaps their most embarrassing setback yet on Thursday. One of their leaders, a Syrian Army defector who recruited them, was abducted in Syria near the Turkish border, along with his deputy who commands the trainees. They were seized not by the Islamic State but by its rival the Nusra Front, an affiliate of Al Qaeda that is another Islamist extremist byproduct of the four-year-old Syrian civil war.

The abductions illustrate the challenges confronting the Obama administration as it seeks to marshal local insurgents to fight the Islamic State, which it views as the region’s biggest threat.

After a year of trying, the Pentagon still struggles to find recruits to fight the Islamic State without also battling the forces of President Bashar al-Assad of Syria, their original foe. The willing few face vetting meant to weed out extremists, so stringent that only dozens have been approved, and they are bit players in the rebellion. The program has not engaged with the biggest, most powerful groups, Islamist factions that are better funded, better equipped and more motivated.