Hamas's representative in the Yemeni capital Sanaa, Mouath Abu Shamala, met Houthi leader Mohammed Ali Al Houthi in his office on Sunday, leading to widespread anger.
Al Houthi was honoured with a Hamas plaque of honour for his support to the Palestinian cause and in recognition of the donation campaign launched by the rebel group to support the Gazan militants financially.
The meeting sparked anger on social media, after which the Palestinian group said Abu Shamala was acting on his own.
A Yemeni politician and member of Parliament, Shouqi Al Qadhi, said on Twitter that he was shocked by the visit and called for an explanation.
Mr Al Qadhi said Yemen’s internationally recognised government could sever ties with Hamas.
“We are waiting for a full clarification regarding its shocking stance. Does Hamas officially represent Abu Shamala?” he said.
Hamadan Al Alyae, a Yemeni journalist, accused Hamas of betraying Yemenis by honouring Houthi militants who have attacked innocent civilians.
Baraa Shiban, a Yemeni expert and consultant, said this was not the first time that Hamas had thanked the rebels.
“Resistance movements and Israel is a cover for repressive movements and sectarian militias, such as Houthis,” Mr Shiban said.
Yemeni journalists and activists on social media slammed Hamas for honouring the Houthi leader and many described it as a "betrayal" of the Yemeni people.
Anis Abdullah, a human rights activist from Aden, said Hamas, the Houthis and the Muslim Brotherhood in Yemen share "the same agenda and the same ideology".
"The three groups have been working for the same project and they switch roles whenever needed " Mr Abdullah said.
Summer Ahmed, a writer and human rights activist from south Yemen, said that the meeting in Sanaa came as a "shock" to many Yemenis.
"It is obvious that Iran is trying to push their proxies, to show that they all support one another," she told The National.
"The meeting came as a shock to many Yemenis who support Hamas and the resistance against the Israeli occupation.
"Many Yemenis had thought that Hamas does not support the atrocities being committed against the people of Yemen, by the Houthis, even though they're supported by Iran too.
“Thus, this meeting was a smack in the face of Yemenis, viewed as if Hamas was rewarding the Houthis for burning children alive and terrorising Yemenis."
Internationally, analysts said that the relationship between Hamas and the Houthis had been growing steadily for some time.
"Hamas leaders had openly praised the Houthis for their support during the latest Hamas-Israel conflict," security analyst Irina Tsukerman told The National.
Iran analyst Jason Brodsky said the Houthis had asked Hamas for logistical advice and offered to co-ordinate attacks on Israel.
"The past meeting between the Hamas representative and the Houthis in Sanaa shows a growing integration of Iran's proxies and partners in the region into an integrated network able to co-ordinate on operations, share best practices and intelligence, and support each other's operations as needed,” Ms Tsukerman said.
“Hamas is more of a partner and less of a proxy for now, but it has welcomed the increase in Iran's funding for its operation and has been increasingly open about their ties," Ms Tsukerman said.
She said the Houthis started out as an ally for Iran's goals in Yemen, but over time have become increasingly dependent on Tehran's orders and ideologically loyal to its spirit and agenda.
After the outrage, Hamas issued a statement on Tuesday praising the Yemeni people for their support to Palestine.
It said any statement or behaviour seen as bias towards any party in Yemen was personal and did not represent the stance of the group.
