After almost half-a-century of conflict, more than two million Filipinos residing in several Muslim-majority regions of the country cast their votes on the establishment of a new Muslim-dominated entity, known as the Bangsamoro (meaning Moro nation), in the southern island of Mindanao.

The crucial referendum comes six years after the historic peace agreement that ended the decades-long war between the Philippine government and Moro Islamic Liberation Front (MILF), and six months after President Rodrigo Duterte signed the Bangsamoro Organic Law.

If approved by the majority in the referendum, the proposed political entity will replace the much smaller Autonomous Region of Muslim Mindanao (ARMM), an earlier experiment at granting political autonomy to limited numbers of Muslim Filipinos, mostly form the Tausug ethnic group.

The ARMM has largely been deemed a failure, perennially hobbled by misgovernance and rampant corruption, and leaving several Muslim-majority regions outside its scope. Both the Philippine government and the rebels, however, hope that the proposed new entity will be more inclusive, sustainable and more competently governed than its predecessor.

The first phase of the plebiscite was held on January 21, covering the ARMM, the ethnically mixed and prosperous cities of Cotabato and Isabela, where voters were asked whether they approved of or wanted their city to be part of the new Bangsamoro entity.

The election went broadly peaceful and was deemed by international observers as credible. The proposition is expected to pass, though partial, unofficial results show, so far, significant opposition to the establishment of the new Bangsamoro entity in places such as Sulu and Isabela City.

The second phase will take place on February 6, covering Lanao del Norte, North Cotabato and other regions that petitioned to be part of the Bangsamoro.

Man of the hour

As the first Filipino president from the island of Mindanao, Duterte made the creation of the Bangsamoro a central theme of his administration. Unlike any of his predecessors and contemporaries, he dedicated both his heart and political capital to ensuring that the Christian-dominated Filipino political elite endorses the Bangsamoro Organic Law (BOL), which was stalled in the Philippine Congress for years.

Surveys suggest that while eight out of 10 Muslim Filipinos favour the creation of the autonomous Muslim entity, among the general population only a small minority (about a third) support the plan.

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For centuries, Muslim Moros have faced systematic discrimination and marginalisation in the Catholic-majority Philippines, largely as a result of the heavy influence of Imperial Spain, a former coloniser notorious for its anti-Muslim prejudice and policies. They have been portrayed as the ultimate "other" in the Filipino psyche and were often caricatured as uncivilised and un-Filipino. Proud of their distinct history and cultural traditions, Moros resisted the rule and influence of Christian-majority national government.

In an act of political courage, Duterte, a nominal Christian, made peace in Mindanao a central campaign promise: "If I become president, if Allah gives his blessing before I die, since I am old, I will leave to you all a Mindanao that is governed in peace." He presented himself as the Moro people's president, who will do his utmost to correct "historical injustices" they have been subjected to at the hands of the Filipino government.

Winning formula

In his second year in office, Duterte convinced the Philippine legislature to pass the Bangsamoro law, which, among other things, granted sociocultural and political autonomy to Muslim-majority provinces in the country, including the establishment of Sharia-based courts.

Crucially, he also made sure that enough resources, including a fifth of national internal revenues, are allocated to assist institution building and the process of political transition.

Now, if the "yes" votes win in the ongoing referendum, the Bangsamoro leadership will also enjoy significant fiscal autonomy, having only to remit a quarter (as opposed to 40 percent for other provinces) of its revenues to the national government, which will maintain control over currency and law enforcement.

The MILF leadership, meanwhile, has conscientiously embraced modern governance, educating many of its best and brightest in public administration colleges. They hope to avoid the mistakes of their predecessors in the ARMM by building a more ethnically-inclusive, geographically expansive and competently-run Muslim-majority autonomous region.

The path forward

While it is likely that the majority of the referendum's participants are going to approve the proposal for the formation of the new Bangsamoro, Duterte and the future rulers of the Bangsamoro still face an uphill battle. Once the new entity is formed, they will have to tackle deep-rooted and complex problems, including high poverty incidence, reconstruction of heavily devastated cities like Marawi and widespread threat of terrorism by armed groups affiliated to the Islamic State of Iraq and the Levant (ISIL, also known as ISIS).

Another area of concern is the fate of minority groups. There has been an influx of ultraconservative Wahabi-Salafist influence in Mindanao in recent years, whether through online indoctrination, Islamic preachers, religious ideologues, or transnational organisations hailing from South Asia and the Middle East.

This caused some to fear that the Bangsamoro may adopt an ultraconservative governing model and may even follow the example of Indonesia's Banda Aceh, an autonomous region governed by Islamic law since the early 2000s, where increasingly draconian laws have been enforced, most especially at the expense of LGBT groups and religious minorities.

There is also the threat of intervention by the Philippine Supreme Court, which declared a previous peace agreement as "unconstitutional" on the grounds that it violates the country's territorial integrity and basic democratic principles. And there are doubts as to whether Duterte's successors will build on his efforts and provide necessary support to future leaders of Bangsamoro when push comes to shove.

What's clear, however, is that the Moros have taken a fateful step towards self-determination and, perhaps, even lasting peace and what we are witnessing is a major turning point in the long-tortured history of Mindanao.

The views expressed in this article are the author's own and do not necessarily reflect Al Jazeera's editorial stance.