His daughter and heir apparent Mehbooba Mufti (above) has so far declined to take the oath as his successor, pushing the state under federal rule.
Mr Sayeed was heading a tricky coalition with India's ruling Bharatiya Janata Party (BJP) - one he stitched together following intense back-door and open negotiations.
In the 2014 state assembly elections, the BJP won 25 seats in the Hindu-dominated Jammu region, while Mr Sayeed's People's Democratic Party (PDP) won 28 in predominantly Muslim Kashmir.
The BJP is perceived as being anti-Muslim by a majority of Kashmiris, and in stitching together the coalition, the PDP ran the real risk of alienating its vote bank.
However, Mr Sayeed justified the alliance, saying he wished to reconnect the religiously divergent regions of Jammu and Kashmir. "I cannot contribute to further dividing the state on communal lines," he told me last year.
At the time, Mr Sayeed not only chose to ignore the popular perception that joining hands with the BJP would open Kashmir to the Hindu nationalist RSS, he went the extra mile by praising Prime Minister Narendra Modi and terming him "not at all communal".
He assured the people of Kashmir that the coalition would deliver its promises, listed out in a document called "The Agenda of Alliance".
However, 10 months of the PDP-BJP rule has not yielded much.
A compensation package to help people affected by the devastating floods of September 2014 was delayed until November 2015 and, when it finally did come, it was not enough.
Apart from a package for Kashmiri Pandits - Kashmiri Hindus who were forced out of the region in the 1990s - and another for refugees from Pakistan-administered Kashmir, all other issues in the document have been ignored.
Although PDP leader Naeem Akhtar has called the document "sacrosanct", the BJP does not seem to regard it that way.
Party members have even gone so far as to challenge Article 35A of the Indian constitution, which bestows special identity on Indian-administered Kashmir - although the document vows to preserve it.
They have also made several contentious statements on Article 370 which gives Kashmir autonomous status.
Given that this is the "baggage" Ms Mufti will have to deal with when she steps into her father's shoes, she is in a serious dilemma.
Insiders believe Ms Mufti - a vocal opposition leader so far - will always be restless while her party is in power.
They say that she was against the alliance with the BJP, but could not express her opposition because of her father.
Today the party has authorized her to decide the future of the alliance.