The attacks are the first claimed by IS - a Sunni group - since it set up a branch in Yemen in November.
Both mosques were used mainly by supporters of the Zaidi Shia-led Houthi rebel movement, which controls Sanaa.
Yemen has suffered from political instability for years and Houthi rebels control nine of the 21 provinces.
The government of internationally recognised President Abed Rabbo Mansour Hadi has fled to the southern port city of Aden.
Four suicide bombers attacked the Badr mosque, in the south of Sanaa, and the al-Hashoosh mosque, in the north of the capital, as worshippers gathered for Friday prayers.
At the Badr mosque, one bomber entered the building and detonated his explosives while other people were caught by the second bomber near the main gates.
Prominent Houthi cleric Al-Murtada bin Zayd al-Mahatwari, the imam of the Badr mosque, was among those killed, local media reported.
Two more bombers attacked the al-Hashoosh mosque, with one detonating explosives near the entrance and the other running into the mosque itself.
"Blood was running like a river," said survivor Mohammed al-Ansi.
Rebel controlled al-Masirah TV broadcast footage from the al-Hashoosh mosque showing volunteers using bloodied blankets to carry away victims. Bodies were also lined up in the prayer hall.
About 300 people were wounded, medics said, and hospitals appealed for blood donors.
There was another suicide attack on a mosque in the northern city of Saada - a Houthi stronghold - reports said, but only the attacker was killed.
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