The Taliban have declared victory over the province of Panjshir northeast of the capital Kabul, the final pocket of territory which has remained outside their rule.
The group posted footage online of their fighters raising their flag there on Monday.
Resistance fighters however said they were still present in “all strategic positions” and “continue to fight”.
Their leader has called for a “national uprising” against the Taliban.
In an audio recording posted on social media Ahmad Massoud, leader of the National Resistance Front of Afghanistan (NRF), blamed the international community for legitimising the Taliban and giving them military and political confidence.
“Wherever you are, inside or outside, I call on you to begin a national uprising for the dignity, freedom and prosperity of our country,” he said.
The Taliban took control of the rest of Afghanistan three weeks ago, seizing the capital Kabul on 15 August following the collapse of the Western-backed government.
It comes nearly 20 years after US forces led an invasion to topple the Taliban.
Panjshir, a rugged mountain valley, is home to between 150,000 and 200,000 people. It was a centre of resistance when Afghanistan was under Soviet occupation in the 1980s and during the Taliban’s previous period of rule, between 1996 and 2001.
“The Taliban haven’t captured Panjshir,” Ali Maisam, spokesman for the NRF, earlier told the BBC, saying he was “rejecting Taliban claims”.
A tweet from the group’s Twitter handle also said: “The struggle against the Taliban & their partners will continue until justice & freedom prevails.”
But Taliban spokesman Zabihullah Mujahid said in a statement that “with this victory, our country is completely taken out of the quagmire of war”.
The National Resistance Front of Afghanistan (NRF) has been resisting Taliban rule
Since taking power the Taliban have sought to portray themselves as more tolerant, but incidents of brutality and repression are still being reported in parts of Afghanistan.
Although the group has promised to respect the rights of women, many fear a return to the way they were treated when the Taliban were previously in power. Women were forced to cover their faces outside, and suffered harsh punishments for minor transgressions.
Witnesses have told the BBC that Taliban militants shot and killed pregnant policewoman Banu Negar on Saturday.
The Taliban told the BBC they had no involvement in Negar’s death and are investigating the incident.
There have also been several protests calling for respect for women’s rights across Afghanistan.
On Monday, a group of women demonstrating in the northern city of Mazar-e-Sharif told BBC Persian that Taliban fighters had threatened them.
“They swore at us and insulted us, and said that we should disperse quickly or else they would beat us to death,” she said, adding that the militants had also threatened anyone who tried to film them.
Women have taken part in protests demanding respect for their rights across Afghanistan
Human rights groups have also documented revenge killings, detentions and persecution of religious minorities. The Taliban have said officially that they will not seek retribution against those who worked for the former government.
As yet the Taliban have not announced the final make up of their new regime.
Spokesman Zabihullah Mujahid told reporters on Monday morning that all the important decisions have already been made, and that they are now working on the “technical issues”.
He also said an interim government would be announced first, allowing for changes later.