For one thing, the merger, announced Tuesday by Iraq's al-Qaida leader Abu Bakr al-Baghdadi, will be a setback for the mainstream rebel forces in Syria, who are largely Sunni but are not militantly Islamic, because it's likely to complicate U.S. and Western support for the main non-jihadist group, the Free Syrian Army.
Despite backing the uprising against Syrian President Bashar Assad, Western governments have shown little enthusiasm for arming the rebel forces, in large part because they fear the weapons will fall into jihadist hands.
The merger was announced one day after the leader of al-Qaida Central, Ayman Zawahiri of Egypt holed up somewhere in Pakistan's badlands, called for an Islamist state in Syria as the precursor to re-establishing the Islamic caliphate that ruled the region the Middle Ages.
His call was widely seen as propagandistic. But the U.S. global security consultancy Stratfor observed: "Baghdadi's statement will worry the international community...
"The formation of this new group attests to growing suspicions that the Syrian jihadists, who could very well outlast the Assad regime, are not nationalistic.
"Rather, they are part of al-Qaida's efforts to exploit the Arab Spring uprisings."
The new alliance, which formalizes an Iraqi-Syrian jihadist coalition that has been widely acknowledged for some time, could also accelerate the destabilization of Iraq.
The fragile, Shiite-dominated Baghdad government of Prime Minister Nouri al-Maliki is already being battered by the Islamic State of Iraq, al-Qaida's Iraqi branch, whose minority Sunni militants are carrying out deadly bombings against the state and the Shiite majority almost at will.
With the Syrian conflict already spilling over into Lebanon, whose fractious government is barely functional and has no prospect of being able to head off sectarian fighting that's steadily gathering momentum, the rest of the region seems to be lurching toward anarchy as well.
The new coalition, which al-Baghdadi announced in a communique, will be known as the Islamic State of Iraq and the Levant. There was no statement from the al-Nusra Front, considered the most effective rebel fighting force in Syria.
That would imply that the Iraqi organization, which has been active for several years and fought the Americans before they withdrew from Iraq in December 2011, is the dominant component of the coalition.
Whether that is so remains to be seen. The Iraqi branch has reportedly supplied battle-seasoned veterans to bolster the al-Nusra Front in recent months, while maintaining its own bombing offensive across Iraq.
Al-Qaida in Iraq opposes Iran's efforts to impose its authority over Shiite-majority Iraq following the withdrawal of U.S. forces, who conveniently got rid of Tehran's archenemy Saddam Hussein in 2003.
Iran is supporting Syria's embattled regime, which is dominated by the minority Alawite sect, an obscure offshoot of Shia Islam.
If the regime in Damascus falls, Iran's ambitions of extending its influence deep into the Sunni-dominated Arab world, and in this case pushing up to the border of Israel, will collapse.
That will leave Tehran's Shiite proxy, Hezbollah, stranded and cut off in Lebanon without the supply lines that run through Syria.
For Israel, an al-Qaida advance to its northern border will mean that the Sunni jihadists, sworn to crush the Jewish state, have simply replaced Hezbollah, which has been the main protagonist on that front since 1982.
The jihadist merger probably will not change much on the ground in either Syria or Iraq in the short term.
But it will have long-term ramifications at a time when al-Qaida appears to be resurgent across the Middle East, and moving into West Africa as well.
Right now, al Qaida forces are engaged in fighting Western, or Western-backed forces, at both ends of the Mediterranean, in Mali, where French troops intervened in January, and in Syria.
The eastern imbroglio threatens to expand into Lebanon and Jordan, both feeble states and easy prey for well-positioned jihadists, as well endanger Turkey and Iraq.
In the meantime, hundreds of foreign jihadists are reported to be pouring into Syria, bolstering the hard-line Islamist forces there.