Ahlu Sunna Wal-jama'ah has accused al-Shabaab of killing its religious leaders and desecrating graves.
Farhan Abdiwali, a Guriel resident, said he had seen 19 people shot dead in the clashes, mostly fighters.
Another resident, Sahra Sheik Muse, said six members of one family had been killed by a mortar shell.
The fighting came as Ethiopian soldiers, who entered Somalia in 2006 to help the transitional government battle opposition forces, continued their withdrawal from the country.
Analysts have said that the Ethiopian pullout could actually weaken al-Shabaab, which used nationalist and religious rhetoric to recruit fighters.
Somalia's transitional government controls only the town of Baidoa, where the parliament is based, and small pockets of Mogadishu, while opposition factions such as al-Shabaab, have seized much of the rest of the country in recent months.
However, there have been several clashes between rival opposition groups in recents weeks. On Saturday, residents of Balad, about 30km north of Mogadishu, reported fighting between al-Shabaab fighters and another group.
Several opposition factions signed a peace deal with the UN-backed government last year, but al-Shabaab refused to take part in the process.
Somalia has been without a functioning central government since 1991. Fighting over the last two years has left at least 16,000 civilians dead and more than one million have fled their homes.