In a report, the New York-based rights group said it had compiled a list of the names of 248 people killed in the two villages in coastal Tartus province on May 2 and 3.
But it said the number was probably much higher, and called the deaths "one of the deadliest instances of mass summary executions since the start of the conflict in Syria".
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HRW said the deaths in Bayda and Banias served as a reminder that other weapons were also being used in Syria's conflict.
"While the world's attention is on ensuring that Syria's government can no longer use chemical weapons against its population, we shouldn't forget that Syrian government forces have used conventional means to slaughter civilians," HRW's acting Middle East director Joe Stork said.
"Survivors told us devastating stories of how their unarmed relatives were mowed down in front of them by government and pro-government forces."
The deaths were widely reported in May, with the Syrian Observatory for Human Rights NGO putting the final tolls at 162 dead in Bayda and 145 dead in Banias.
The group says at least 110,000 people have been killed since the conflict in Syria began in March 2011.
Earlier this week, UN investigators said forces loyal to President Bashar al-Assad "have continued to conduct widespread attacks on the civilian population, committing murder, torture, rape and enforced disappearance as crimes against humanity".
The villages of Bayda and Banias are majority Sunni, while the areas surrounding them are largely Alawite -- the religious minority to which Assad belongs.
The deaths were denounced at the time by the Syrian opposition as a "sectarian massacre".
HRW said that most of those killed were executed after military clashes between rebels and government forces had ended.
In Bayda, "the forces entered homes, separated men from women, rounded up the men of each neighbourhood in one spot, and executed them by shooting them at close range," the group said.
"Human Rights Watch also documented the execution of at least 23 women and 14 children, including infants," the report said.
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