Anglesey was merged with the mainland areas of Caernarfonshire, Merioneth, and part of Denbighshire to become a new county called Gwynedd.

During the transition to the new system, the shadow authority requested a change of name in both languages, to "Isle of Anglesey" in English and "Sir Ynys Môn" in Welsh.

[9] Since 1996 the local authority has therefore been "Isle of Anglesey County Council" in English, and "Cyngor Sir Ynys Môn" in Welsh.

[12] In March 2011, after "years of political infighting", it became the first council in British history to have all executive functions suspended, with a team of commissioners appointed by the Welsh government put in place to run the council's functions,[13] with elections ultimately delayed,[14] meaning they took place a year after the rest of Wales, pending a new electoral system.

[17] In February 2019 the council reported that North Korea was likely to have been behind a cyberattack on its systems, carried out through a proxy ISP (IP) address based in Japan.

Experts suggested that Anglesey was not likely to have been the specific target, with the hackers engaged in a broader attack on UK government infrastructure.

[18] In 2022, as part of the Levelling Up White Paper, an "Island Forum" was proposed, which would allow local policymakers and residents in Anglesey to work alongside their counterparts in Orkney, Shetland, the Western Isles and the Isle of Wight on common issues, such as broadband connectivity, and provide a platform for them to communicate directly with the government on the challenges island communities face in terms of levelling up.

However, in 2010 the council leader, Clive McGregor, left the Original Independents to form Llais Môn[23] (meaning Anglesey Voice) who had five members by the time of the 2013 election.

[26] The 2017 Isle of Anglesey County Council election on 4 May resulted in a no overall majority position with Plaid Cymru holding 14 of the 30 seats.

The 2022 Isle of Anglesey County Council election on 5 May resulted in an overall majority with Plaid Cymru holding 21 of 35 seats.