Denang Sangma, who led the alliance of the National People's Party (NPP), BJP and GNC members of the 29 member House resigned after the Chairman Boston Marak of the alliance switched sides to join the rival Congress.
Boston had yesterday allowed a No-Confidence Motion to be moved.
The Chief Executive Member resigned ahead of a No-Confidence test he was to face on the floor of the House today.
Denang handed over his resignation to Chairman Boston Marak. He, however, did not attend the debate on the second date of the ongoing budget session. The budget too was not passed after the executive committee was dissolved.
Denang earlier had the support of 19 out of the 29 members in the House. But six members including Marak defected to the Congress.