Ayman Al-Zawahiri, the leader of al Qaeda, broke a record 11-month silence this week, issuing a video proclaiming his loyalty to the new head of the Taliban, Mullah Akhtar Mansoor.
After the announcement last month that Taliban founder Mullah Mohammad Omar died two years ago, some experts wondered if Al-Zawahiri was also dead.
Omar's death also raised questions about whether that would make the group more likely to reconcile with the U.S.-backed government in Kabul.
However, Bruce Riedel, a Brookings Institution senior fellow and former CIA official, called the reaffirmed alliance between al Qaeda and the Taliban "a set back."
"The almost 10-minute long message dramatically reaffirms the alliance between al-Qaida and the Taliban, a setback for efforts to bring the Taliban into a political process," he wrote in Brookings piece Thursday.
One of the U.S.-supported conditions for reconciliation is for the Taliban cut ties with al Qaeda.
Riedel said the Taliban may return to talks with Kabul, but "it is not likely to accept a cease fire or break its decades old ties to al-Qaida," Riedel said.
Furthermore, he added, al Qaeda's media arm, As-Sahab, has moved from Pakistan back into Afghanistan's Helmand province, where thousands of U.S. troops fought to push out the Taliban during a surge ordered by President Obama.
"The Afghan Taliban supported the move and provides safe haven for al-Qaida, which means 14 years after Operation Enduring Freedom began, al-Qaida is again running operations out of Afghanistan," Riedel said.
"Al-Zawahri's message underscores that al-Qaida remains close to the Taliban," he said.
Riedel said in a warning to the United States, Al-Zawahiri said, "Our common enemy does not know what is coming its way."
Perhaps in a slight to the Islamic State in Iraq and Syria (ISIS), Al-Zawahiri in his message lauded Omar for creating the first true Islamic emirate since the fall of the Ottoman Empire a century ago.
ISIS has established a presence in Afghanistan and is battling the Taliban for influence and land. Although ISIS grew from al Qaeda in Iraq, it sees itself as a rival to al Qaeda, and the two groups are competitors.
Al-Zawahiri did not mention ISIS or its leader, Abu Bakr al-Baghdadi, who has proclaimed himself the Caliph Ibrahim.
According to Riedel, the message was: "Mansoor is the rightful leader of the global jihad for al-Zawahri; al-Baghdadi is an upstart who is not worthy of comment."