The MQM has been a vocal critic of the Tehrik-i-Taliban Pakistan (TTP) and had organised a huge rally last month to condemn the Taliban attack on a 15-year-girl Malala Yousafzai in Swat valley.
MQM leaders also claimed that Taliban have sneaked into Karachi, its stronghold, and involved in terrorist and criminal acts.
"We have decided to deal with the brutal, apostate MQM, which has occupied Karachi. We will show no mercy on the group," Taliban spokesman Ehsanullah Ehsan said in a statement.
"We have taken the decision to free the oppressed people of Karachi from the hold of the tyrants. We are with every oppressed people," he said.
The Pakistani Taliban spokesman also announced opposition to the upcoming parliamentary elections.
Besides, he supported the nationalist groups in Balochistan and Sindh provinces including the Baloch Liberation Army and Sindh Liberation Army, who are routinely targeting the security forces. He advised these groups to fight for their rights in line with Islamic principles.
The spokesman also called out to Pakistan's judges to work for an Islamic system.