The Iran-backed Shiite rebels detained 35 people between August 2014 and October 2015, the rights group said, adding that 27 remained in custody.
It said many of the detainees appeared to have links to the Islah Sunni Islamist party, a rival of the powerful rebels.
"Huthi arrests and forced disappearances of alleged Islah supporters have generated palpable fear in the capital," said Joe Stork, HRW's deputy Middle East director.
"Politicians, activists, lawyers, and journalists tell us they've never been more frightened of ending up 'disappeared,'" he said.
Signup to our newsletter and follow us on Facebook and Twitter!
Aided by troops loyal to ousted president Ali Abdullah Saleh, the Huthis overran Sanaa unopposed in September 2014, and went on to expand their control over several regions.
A Saudi-led coalition launched a military campaign against the rebels in March after the insurgents advanced on the southern city of Aden, where President Abedrabbo Mansour Hadi took refuge before fleeing to Riyadh.
"At a time when the Huthis are fighting to remain key power brokers in Yemen, they should recognise that instilling fear in the population is no way to govern," Stork said.
"The Huthis should take the necessary steps to ensure that no one is held unlawfully and families have access to their loved ones," he said.
A fresh round of UN-sponsored talks to end the Yemen conflict is due later this month in Geneva.