The capture of Mannagh could now free hundreds of opposition fighters to reinforce other fronts, including the sieges of the nearby Shiite-majority towns of Nubul and Zahra, which are in regime hands.
Syria's conflict has taken on an increasingly sectarian tone in the last year, pitting predominantly Sunni Muslim rebels against members of Assad's Alawite sect, an offshoot of Shiite Islam.
In the predominantly Alawite province of Latakia on the Mediterranean coast, the rebels captured 11 villages, edging closer to Assad's ancestral home in the region, the village of Qardaha.
The opposition's gains in Latakia, an Alawite stronghold that has been peaceful for much of the Syrian conflict, is a symbolic blow to the regime and a boost to the rebels.
But those gains have been overshadowed by reports from activists that more than 80 people were killed in two of the villages overran by opposition fighters. The activists spoke on condition of anonymity for fear of reprisals. If confirmed, the slayings will likely deepen Syria's sectarian strife.
Syria's crisis started as largely peaceful uprising against Assad's rule in March 2011 but turned into a civil war after opposition supporters took up arms to fight a brutal government crackdown. More than 100,000 people have been killed in the violence.
The SNC on Tuesday accused the government of carrying out several "massacres" during the holy month of Ramadan alone, killing hundreds of civilians.
The Observatory reported heavy fighting in Latakia throughout Tuesday while SANA said the army launched a counter-offensive and by evening, recaptured two villages. There were no immediate reports of casualties.
Also Tuesday, pro-government daily Al-Watan said rebel kidnapped Sheik Badreddine Ghazal, a prominent Alawite cleric in Latakia region. The paper said he was taken Monday from the village of Barouda, one of those captured by earlier rebels.
A government official in Damascus confirmed Ghazal's abduction saying the cleric was "severely beaten" by his captors. The official, who spoke on condition of anonymity in line with regulations, did not give further details.
Associated Press writers Albert Aji in Damascus, Syria, and Bassem Mroue in Beirut contributed to this report.