The Middle Eastern group, also known by its Arabic acronym Daesh, has never formally acknowledged having a presence in Afghanistan but fears are growing that the group is making inroads in the country.
In a letter addressed to ISIS leader Abu Bakr al-Baghdadi, the Taliban insisted that "jihad" (holy war) against the Americans and their allies must be conducted under one flag and one leadership".
"The Islamic Emirate (Taliban) does not consider the multiplicity of jihadi ranks beneficial either for jihad or for Muslims," said the letter signed by the Taliban deputy leader Mullah Akhtar Mohammad Mansoor.
Taliban leader Mullah Omar
"Your decisions taken from a distance will result in losing support of religious scholars, “mujahideen”... and in order to defend its achievements the “Islamic Emirate” will be forced to react," it added.
The letter, published on the Taliban website in Pashto, Urdu, Arabic and Dari, did not elaborate on its threat.
The Taliban have seen defections in recent months -- with some insurgents apparently adopting the ISIS/ISIL flag to rebrand themselves as a more lethal force in Afghanistan.
The two groups, which espouse different ideological strains of “Sunni Islam”, are believed to be arrayed against each other in Afghanistan's restive south, with clashes frequently reported.
Last week, local media reported pitched battles between the Taliban and supporters of ISIS in eastern Afghanistan, with casualties reported on both sides.
General John Campbell, the commander of NATO forces in the country, last month said the ISIS group was recruiting fighters in Afghanistan but they were not yet operational.
There have been fears of ISIS group making inroads in Afghanistan after 13 years of fighting the Taliban in the Afghanistan.
In February, a NATO drone strike killed Mullah Abdul Rauf Khadim, a former Taliban commander and Guantanamo detainee with suspected links to ISIS, in the volatile southern province of Helmand.
And in March Hafiz Waheed, a successor to Khadim, was killed along with nine others in the Sangin district of Helmand, according to the Afghan defence ministry.
It is not known whether the men had the official sanction of ISIS, which announced its presence in South Asia a year ago