Five days into a new year, the year that was to mark Iran's re-entry into the international community, and relations between two of the Middle East’s most important countries have fallen to their worst level in decades.

After Saudi Arabia executed 47 men convicted of terror-related offences, including Nimr Al Nimr, a dissident Shia cleric, the Saudi embassy in Tehran was ransacked and in response Saudi broke off diplomatic relations with Iran. In what will be a pivotal year for the region, relations between these two countries have started from a low point.

But the reaction to the execution of Al Nimr also points to something of far greater import. What has become starkly apparent in the past few days is how rapidly lines of allegiance are shifting across the region. In a way, who is criticising Saudi Arabia is more consequential than what they are saying.

The three strongest reactions came from Iraq's former prime minister Nouri Al Maliki (who declared Al Nimr's death would "topple the Saudi regime"), Hizbollah (an "assassination") and Iran's Supreme Leader (who warned Saudi's rulers would face "the divine hand of revenge").

On the one hand, this should be puzzling. Why is the former prime minister of one country criticising the internal court decisions of another? Why is a militant group that styles itself as the defender of one country concerned about a citizen of another?

What they have in common is that they all represent Shia religious communities – that is, they all see themselves, in part, not merely as defenders of a national or political community, but as defenders of a religious one.

Hizbollah say they need to retain their weapons to defend Lebanon from Israeli attack – but then use those weapons to defend a minority Shia regime in Syria. Nouri Al Maliki, who obviously has aspirations to return to the prime ministership of Iraq, is shoring up the vote of his Shia constituents. Rather than portraying himself as a national, Iraqi leader, he openly appeals over the heads of Christian, Sunni Muslim and other Iraqis to focus on one sect alone.

The most worrying is Iran, which explicitly sees itself as the leader of a religious community, not merely of its own citizens. There are Shia communities around the Muslim world: they are Arabs and Iranians, Azeris and Indians, Afghans and Turks. They live in a dozen countries. If Iran claims to speak on behalf of Shia communities, it gives itself the right to interfere in the affairs of many independent countries.

More than anything else taking place today in the Middle East, the normalisation of sectarian identity, and political appeals to loyalty based on that identity rather than citizenship, is the most dangerous aspect of this new century. Left unchecked, it will define the region for decades, and potentially tear once mixed communities apart. Indeed, it has already done so.

What started as a rhetorical device has become a reality. The sectarian divide has always been overstated, a transposing of the Protestant-Catholic wars of Europe to the Middle East. There has never been a hundred years Sunni-Shia war, let alone 1,000.

But there is little doubt that many people believe in the sectarian divide. The motivation to see in the political decisions of governments the shadow of sectarianism is real, and growing.

It has happened, most of all, in Iraq. That, looking back, will come to be seen as the beginning.

The breaking apart of Iraq in the 2003 invasion created the conditions for the current sectarian war. Certainly, Iran had been using the religious card as a recruiting tool for years – all the way back to the formation of Hizbollah in the 1980s. But Iraq was when it went mainstream.

In the chaos that followed the invasion, communities had to find rapid, easily understandable ways to stick together. Remember that Iraq was insecure: militias of dubious provenance were showing up in towns and cities, manning checkpoints and knocking on doors in the middle of the night.

At that point, for Iraqis, with the men with guns at the door, there was little time for a discussion about the minutia of religion or who prays how.

There was no time for an unpicking of paternal and maternal bloodlines (Sunnis and Shia freely intermarried in Iraq before 2003). There was only protection, and the comfort of sect.

Since then, sect has proven a powerful recruiting tool. There are simply not enough politicians able to garner a platform who speak the language of inclusion. In times of strife, those who speak the language of division always find it easier to get a hearing.

Sectarian feelings have long existed in the Middle East. In the recesses of the mind, that marker of difference, that safety of sect, has always existed. It is the Middle East's equivalent of European racism, to be brought back at times of stress. Sect just needed a political moment.

"Nothing," as the Palestinian-American poet Hala Alyan wrote in a different context, "is as dangerous as an unlit match." After Iraq, sect found its moment.

falyafai@thenational.ae

On Twitter: @FaisalAlYafai