is from the nation's south, a relatively wealthy and majority Christian region that holds most of the country's oil riches.
As vice president several years ago Mr. Jonathan helped resolve a raging insurgency in the southern Niger Delta — at a time when militias were driving up world oil prices with large-scale attacks on petroleum installations.
He was part of negotiations and an eventual amnesty with rebels, some of whom came from his own tribe.
But today Jonathan faces a northern-based militant group, Boko Haram that is killing and kidnapping civilians in a Muslim-majority region. The group's goals and ideology are completely different from the southern militants, something Jonathan has experience with.
With Boko Haram still holding kidnapped school girls, with some 2,000 civilians killed since January, and with a string of gory attacks this week on villages in the northeast – many Nigerians argue that Jonathan's background in the south is leading him astray in his approach to the north and encouraging fresh recruits to join Boko Haram.
"He wanted to take the same model they've used in the Niger Delta, but unfortunately that model will not work [with Boko Haram]," says Dung Pam Sha, director of the office of research and development at the University of Jos in central Nigeria.
Last May, Jonathan imposed emergency rule on three northeastern states, triggering an air and ground military assault that flushed Boko Haram fighters from their camps.
The same strategy was used by Umaru Yar'Adua, Jonathan's predecessor, in the south in May 2009. At that time, thousands of militants accepted President Yar'Adua's amnesty offer, laid down their arms, went into training programs, and took a monthly stipend. Even though some of the former militants say the program isn't fully implemented and while some gangs are resorting now to oil theft from pipelines, the amnesty brought a peace that has largely persisted.
Jonathan has tried a similar bid for reconciliation in the north. On May 29 on national TV he held out a readiness to “accept unconditional renunciation of violence by insurgents, and to ensure their de-radicalization, rehabilitation and re-integration into the broader society."
Yet since, Boko Haram has conducted only more deadly and ruthless attacks.
When Jonathan dealt with the southern rebels the demands were mostly economic. They were fighting for more oil revenue to be shared with their communities. While the most organized rebel group, the Movement for the Emancipation of the Niger Delta, or MEND, didn't accept the amnesty, thousands of other fighters disarmed.
By contrast, Boko Haram is in one of the poorest regions of Nigeria. The group’s main grievances, moreover, derive from a view that Nigeria's woes are due to the western influences that came with British colonization. Nigeria’s corruption and poverty, they say, can only be fixed by the creation of a caliphate employing a strict interpretation of Islamic law – and they're intent on destabilizing the government in Abuja to accomplish that end.
Another difference for Jonathan is that, thanks to his roots, he often knew southern rebels and had ties to them. He has no such connections in the north. Further, the “old boy” network of political elites in the south were often spared by rebels. In the north only last week, by contrast, Boko Haram killed a senior traditional ruler, the Emir of Gwoza, Alhaji Idrissa Shehu Timta — bringing fear to the establishment.
"He [Jonathan] sees the Niger Delta as a problem he contained because of his links to the Niger Delta and his access to the militants," says Clement Nwankwo, executive director of Abuja-based Policy and Legal Advocacy Center. "He thinks that the political elites from the north who are his friends and who he has brought to be ministers or advisers, should necessarily have links with Boko Haram."
Finally, it seems doubtful that Boko Haram is likely to be as easily mollified as the southern rebels.
As the International Crisis Group notes in an April report, the Jonathan administration should recognize “that unless issues of bad governance and systemic corruption are addressed vigorously and transparently, all other measures will be nothing but stop-gaps."