KABUL, Afghanistan — Since he first picked up a gun as a 15-year-old, Abdul Basir has killed a lot of people. Yet the operation on Friday night was different: He was out to kill his son.

Around midnight on Friday, Mr. Basir, now in his 40s and the commander of a government militia in the northern Afghan province of Faryab, arrived at a compound in an area called Zyaratgah, part of the restive Qaisar District. He had intelligence that his 22-year-old son, Said Muhammad, a hardened member of the Taliban, was there with several of his fighters.

In Afghanistan’s long war, Mr. Basir’s determination to kill one of his children was not unique, but rather just another sign of how long the violence has dragged on, and of how it has permeated the deepest levels of society and poisoned the closest of relationships.

Framed by grand ideologies and elaborate strategies at the top, the perpetual conflict has divided families for a generation. Guerrillas who took up arms against the Soviet occupation became sworn enemies of their Communist relatives. Now, a government commander was hunting down a son who had denounced him as an infidel and forced him from their family’s ancestral village.