One suicide bomber struck inside Badr mosque in southern Sanaa while another targeted worshippers as they fled outside, witnesses said.
The third suicide bomber targeted Al-Hashahush mosque in northern Sanaa.
The Huthi militia's Al-Massira television said hospitals in the capital had made urgent appeals for blood donations.
Leading Huthi cleric Al-Murtada bin Zayd al-Muhatwari, the imam of the Badr mosque, was among those killed, a medical source said.
Medics at three main hospitals in Sanaa told AFP they counted 55 people dead and 83 wounded.
Footage aired by Al-Massira showed bodies lying in pools of blood outside the mosques, as worshippers rushed the wounded to hospitals in pick-up trucks.
There was no immediate claim of responsibility.
Another suicide bomber blew himself up outside a mosque in the northern Huthi stronghold of Saada, a source close to the militia said.
Only the assailant was killed in that explosion and tight security at the mosque prevented the bomber from going inside, the source added.
The Huthis overran Sanaa in September and have since tightened their grip on power.
Their attempts to extend their control into other areas have been met by deadly resistance from Sunni tribes and Al-Qaeda.
Yemen's top security body blamed Al-Qaeda for a car bomb in January that killed 40 people and wounded dozens more at a police academy in Sanaa as recruits lined up to register.
But a leader of the jihadist network denied responsibility at the time.
Front line in the US war on Al-Qaeda
Al-Qaeda in the Arabian Peninsula (AQAP) is regarded by the United States as the extremist network's deadliest branch.
Yemen, a front line in the US war on Al-Qaeda, has descended into chaos since the 2012 ouster of longtime strongman Ali Abdullah Saleh, who has been accused of backing the Huthis.
President Abedrabbo Mansour Hadi escaped Huthi house arrest in Sanaa last month and fled to the southern city of Aden, where violence has erupted in recent days.
A security official said Friday that a top Yemeni officer linked to the Huthis had escaped an assassination bid near Aden overnight.
Four people were killed in an ambush on the Lahj-Taiz road but General Abdel Hafedh al-Sakkaf, the special forces chief in Aden, escaped unharmed, said the official from Lahj.
He said the attack took place in Al-Athawir as Sakkaf fled Aden in a convoy to Lahj, on its way towards militia-held Sanaa.
"He escaped the assassination bid but a bodyguard was shot dead, while three others died when their vehicle overturned," the official said.
Situation calm
The attack came as forces loyal to Hadi tightened their control over Aden where the situation was calm early Friday.
Troops loyal to Hadi and their allied Popular Committees paramilitary manned checkpoints, an AFP correspondent reported.
Hadi himself had to evacuate a presidential palace in Aden on Thursday after a fighter jet opened fire, hitting a nearby hill.
At least seven special forces fighters and four members of the Popular Committees were killed in clashes in Aden on Thursday, security sources said, and 54 were wounded on the two sides.
The violence forced the closure of the city's airport, which Sakkaf's forces tried to seize but were repelled by pro-Hadi troops and paramilitaries.
Following the Huthi takeover of Sanaa, Saudi Arabia and other Gulf countries moved their embassies to Aden and several Western missions closed their doors in the capital because of security concerns.
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