Air strikes may spell end of what has often looked like a mutually beneficial relationship between Syrian regime and jihadists

Bashar al-Assad's enemies often accuse him of being in cahoots with jihadis, but that is not the message of the latest Syrian air force raids on Isis targets – welcomed from Baghdad on Thursday by a grateful Nouri al-Maliki.

Air strikes on al-Qaim, Rutba and al-Walid matched a pattern begun this month with attacks on Raqqa, Hasakah and Deir el-Zour – Isis-held areas of north-eastern Syria that are close to the border with Iraq, now breached wide open to allow allowing the group to move men, money and equipment both ways. Assad and Maliki seem to have simply united against a dangerous common enemy.

Officials in Damascus hotly denied sending fighters into Iraqi air space, presumably to keep up appearances about respecting national sovereignty. But in the new reality of this volatile and dangerous region borders have become little more than lines in the sand – or in the air.

The Syrian attacks might spell the end of what has often looked like a mutually beneficial but opportunistic relationship between a secular Syrian government and intolerant jihadists.

As Isis has become more self-reliant and self-financing, it has arguably become more of a threat than an asset to Assad. Its goal of a fundamentalist Islamic caliphate would mean the destruction of the modern Syrian state that was created in the aftermath of the first world war and the collapse of the Ottoman empire.

When Assad freed hundreds of hardened Salafi fighters, in 2011 and 2012, many of whom had previously been allowed, with the help of the Syrian Mukhabarat intelligence service, to cross into Iraq to fight US forces there, his intention was probably to bolster the narrative that Syria was engaged in a fight against violent extremism. Winning the propaganda war would ward off western help for the moderate opposition and cause damaging divisions in rebel ranks.

Isis has regularly fought the Free Syrian Army or other non-jihadi units. And Isis targets have rarely been hit by the Syrian air force – a conspicuous omission, analysts say.

Proof is elusive, though no one doubts that the Mukhabarat has infiltrated extremist groups, some financed from Saudi Arabia or Kuwait, and is adept at the kind of shadowy manipulation familiar from the Algerian insurgency of the 1990s.

In recent months accusations have multiplied that Isis and the rival Jabhat al-Nusra, both linked to al-Qaida, have been financed by selling oil and gas from wells under their control to and through the regime. Sceptics counter that these arrangements reflect the exigencies of a war economy, not a sinister conspiracy. The issue is hotly debated.

Details of the latest attacks were sketchy, though suspicions of collusion lingered over the previous Syrian air raids. Isis fighters in Raqqa inexplicably left their barracks 24 hours before an attack just after the fall of Mosul. In Deir el-Zour Syrian planes had seemed to fly into Iraqi airspace, suggesting collaboration with Baghdad.

The Syrian National Coalition, the main western-backed opposition group, dismissed those raids as "a ridiculous decoy" designed to rebuild trust with the international community after Assad's clandestine relationship with Isis was exposed.

But a plausible explanation could be that recent developments in Iraq have forced the Syrian president to take Isis more seriously than he has done so far. Tacit cooperation with a dangerous enemy may now be over. If war makes for strange bedfellows, neither party should be too surprised if, when the relationship outlives its usefulness, the other one simply kicks them out.