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".
The report comes as the international community discusses a plan for Syria to turn over its chemical weapons, after an alleged chemical attack that killed hundreds of people on August 21.
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.
HRW said witnesses described pro-government forces burning dozens of dead bodies, as well as burning and looting homes after the executions.
The report said that both regular government troops and members of the pro-regime militia known as the National Defence Force had taken part in the killings.
"In some cases, government and pro-government forces executed, or attempted to execute, entire families," the group said.
In one case documented in Bayda, 26 members of one family - nine men, three women and 14 children - were executed.
The sole survivor was a three-year-old girl who was reportedly wounded by three bullets, but lived.
HRW called on the United Nations to refer the situation in Syria to the International Criminal Court (ICC) and insist that Damascus cooperate with a UN inquiry.
"The Security Council has the opportunity to deter future killings - not just by chemical weapons, but by all means and by all parties - by referring the situation to the ICC," Stork said.
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How very Assad of it!!!Killing unrarmed citizens of your own,just because they happen to be a different sect.