She lost her seat in the 2007 Welsh Assembly Elections, to Conservative candidate Angela Burns.

[12][13] Allies of Gwyther, as well as presiding officer Dafydd Elis-Thomas, argued that misogyny played a strong role in her treatment.

[16] In September 1999, in collaboration with Scottish Agriculture Secretary at the time Ross Finnie, Gwyther obtained £20m of financial support for Welsh sheep farmers from Westminster Agriculture Minister Nick Brown, after significant reductions in the price of ewes lead to challenges for farmers.

[20][21][22] Gwyther later alleged she had privately been given the green light for the scheme by Fischler, who then changed his mind.

[23] A censure motion was passed in the Assembly over the scheme not being secured, but Gwyther retained the support of Welsh Labour and of the Cabinet, and did not resign.

[9][15][25] Presiding Officer Dafydd Elis-Thomas later said he thought there was an "element of sexism in relation to the agriculture secretary" during the debate on the motion.

[26] On 29 March 2000, the Assembly Agriculture and Rural Affairs committee recommended that she block the use of GMOs.

[27] A censure motion was proposed against Gwyther for "for her failure to address the concerns of the National Assembly for Wales, by failing to secure a GM free environment".

On 25 July 2000, on the eve of the Royal Welsh Show, she was dismissed from her post by First Minister, Rhodri Morgan, and replaced by Carwyn Jones.

[23] Gwyther was elected chair of the Economic Development and Transport committee in May 2001, after Val Feld stood down from the role due to illness.