Islamic fundamentalists emerged as a militarized group after the downfall of Somalia's last government in 1991. The militant al-Itihaad al-Islamiya group was dominated by members of the southern-based Hawiye clan, and in Puntland, al-Itihaad could not fully secure the popular support it needed to strengthen their position in a region dominated by the Darod, a rival clan.

In the early 1990s, Abdullahi Yusuf, a Darod military strongman who later became president of Puntland, led a bloody military campaign against the Islamist movement. Al-Itihaad was defeated in Puntland and forced to retreat from all major towns in the region, including Garowe and Bosasso.

Hogendoorn says with the growing power and influence of al-Shabab in the south, there are indications that radicals in Puntland are seizing the opportunity to challenge Puntland's secular authorities.

"The precursor to al-Shabab, al-Itihaad - they were not driven out. They were just driven underground," said Hogendoorn. "Most likely, they communicate with elements of al-Shabab in south-central Somalia. What we have no idea is whether or not this violence is being coordinated by al-Shabab. From my perspective, I have a hard time believing that. I think it is people within Puntland, who are taking the initiative to target the government and try to undermine it."

Al-Shabab militants, who proclaim allegiance to al-Qaida, currently control large areas of southern Somalia and most districts in the Somali capital, Mogadishu. In recent months, the group, listed as a terrorist organization by the United States and Australia, has captured international attention by recruiting fighters from the Somali Diaspora in the United States, Canada, and Europe.