Al-Zawahiri says fighters must ``rise above organizational loyalties and party partisanship'' and unite behind the goal of setting up a state which the group seeks to form after Syrian government is toppled down.
AL-Qaeda affiliated groups have been fighting along the US-backed militants in a massive insurgency that has already killed more than 100,000 people according to the UN.
Al-Zawahiri however suggested he would not impose unity, saying in an audio message Friday that ``what you agree upon will also be our choice.''
The war in Syria started in March 2011, when pro-reform protests turned into a massive insurgency following the intervention of Western and regional states.
Since the start of the war al-Qaeda affiliated groups have been emerging under different names in Syria, fighting at the side of the US-backed opposition which is leading one of the bloodiest conflicts in recent history.
Jabhat al-Nusra and the Islamic State of Iraq and al-Sham (ISIS) are the two main militant groups fighting for al-Qaeda in Syria.
The first is commanded by a Syrian and the second by an Iraqi, but both are loyal to al-Zawahri.
The US-backed Syrian opposition is increasingly losing internal support for taking in al-Qaeda linked groups.
The opposition which is suffering from deep divisions and rivalries, recently blew international efforts for holding the Geneva-based talks aimed at ending the bloody conflict.
The groups said it would not negotiate unless a date is set for Assad to leave.
SHI/SHI