BAMAKO, Mali -- Voters trudged through red muddy roads in Mali's rainy capital Sunday to choose their next president, a leader who will be tasked with reconciling the country after a coup, separatist rebellion and an Islamic insurgency unraveled one of West Africa's most stable democracies.

The presidential runoff vote between former Prime Minister Ibrahim Boubacar Keita and former Finance Minister Soumaila Cisse is aimed at unlocking some $4 billion in aid that has been promised to help Mali recover. The funds, though, are contingent on a democratically elected government being in place.

Keita, known by his initials "IBK," has run on a campaign of restoring Mali's honour after a French-led military operation forced the jihadists into the desert earlier this year and paved the way for the Malian military to return to the northern cities it had fled in the wake of the 2012 Tuareg rebellion.

Among the first voters in line at one Bamako polling station was Amara Traore, 65, whose orange boubou -- a traditional robe -- stood out in the early morning rains Sunday.

"I've been here since 6:30 a.m. with great joy, despite the rain, to elect a president who can better lead the country," said Traore, who said he was backing Keita. "We are tired of this crisis and the insecurity we have been living with."

Keita also has drawn supporters in the northern town of Gao, where just six months ago suicide bombers were launching attacks and jihadists were battling Malian troops in the heart of downtown.

Gao resident Moussa Tahirou Maiga said despite security improvements, the city's economy remains paralyzed and many are looking to Keita to create jobs.

"He has shown his patriotism," said Maiga, 35, who teaches information technology. "He's viewed here as the man who can change a lot of things."

Keita cast his ballot Sunday in Bamako morning and praised voters for coming out to the polls.

"People are saying 'Will the turnout be what we hope?' but I am certain it will be," Keita told reporters. "And the rain here is a blessing and a good sign."

Turnout in the first round of voting was nearly 50 per cent, though in the northern provincial capital of Kidal where rebel flags still fly, it was a mere 12 per cent. Separatist sentiment there remains high, though some within the National Movement for the Liberation of the Azawad had endorsed Keita because of his promise to hold a national dialogue on the crisis there.

On Sunday, local election official Fadimata Maiga said polls had opened on time in Kidal. "Turnout appears to be better than the first round," she said.

Heavy rains kept many polling stations from opening on time Sunday in the capital.

"There's a possibility the governor will extend the polling stations' closing hours if he deems it necessary," said Issaga Kampo, vice-president of the National Independent Electoral Commission.

In the first round of voting, technical glitches kept many from casting ballots. Voters showed up at polling stations only to find their names were not on the list. Others encountered difficulties obtaining their voting cards ahead of the July 28 first-round ballot.

Campaigning ahead of the second round was low key because it coincided with the end of the Muslim holy month of Ramadan.

The presidential election is the first since the separatist Tuareg rebellion in northern Mali in early 2012 sparked anger within the military and led to a March 2012 coup that overthrew longtime President Amadou Toumani Toure. The chaotic aftermath allowed the separatists, and later Islamic extremists linked to al-Qaida, to grab control of northern Mali, an area the size of France.

The French-led military offensive sidelined the radical militants though secular rebels have moved back into Kidal, where they maintain a hold despite the return of the Malian military to the area. Talks with the Tuareg rebels, who want to have an independent area they call Azawad, will be among the first challenges to face the new president.

Also of key importance will be finding a way home for the nearly 200,000 Malians who remain refugees in neighbouring Mauritania, Niger and Burkina Faso. Tens of thousands of northerners also poured into the southern capital of this mostly moderate Muslim nation to flee the violence and harsh Islamic Shariah law in which extremists meted out punishments like amputations for alleged thefts and whippings to women who went in public without their heads covered.

The United Nations refugee agency said initial estimates indicated only about 1,220 of them voted in the first round, though election materials also were being flown in for the second round poll.