The rare public case by pro-Kiev authorities against their own troops comes in the wake of international rights groups' condemnation of both sides' alleged use of torture and other intimidation tactics in the 14-month war.
The Donetsk regional prosecutor's office said the two men had been charged with premeditated murder -- a crime that could put a person behind bars for anywhere between seven years and life.
It said in a statement that the 77-year-old mother and her 45-year-old daughter had been slain by machinegun fire in their own home in the pro-Russian rebel controlled town of Luganske on Monday.
It said both suspects were in their 20s but disclosed no other details.
The Ukrainian conflict has claimed the lives of nearly 6,500 people and driven more than a million from their homes.