Glenn Elder, who was first elected in 2012, will now sit as an independent member on Glasgow City Council after submitting a letter to leader Susan Aitken today.
The SNP took power as a minority administration at Scotland's biggest council in 2017, ending four decades of continuous Labour rule in the city.
But Mr Elder, who represents the Linn ward, said the Nationalist group had since 'lost focus'.
In his letter, he said: “Any criticism of direction is responded to with unconcealed hostility, promoted by you (Susan Aitken) and those close to you. I now believe that I have no choice other than to resign the whip and my SNP membership.
“I still fully believe in the core tenet of the SNP, that of an independent Scotland. Sadly, I cannot, now, be a member of a group that I believe has lost that particular focus, deviating towards personal agendas and being prepared to use bullying and harassment in order to ensure obedience."
Commenting on Mr Elder's decision to resign, Glasgow Labour group leader Frank McAveety said: "I want to congratulate our colleague Glenn Elder on standing up to bullying and harassment. This cannot have been an easy decision for him. His contribution to the city is appreciated across the chamber.
“In his letter, he has laid bare a culture of bullying and harassment. This is deeply concerning. For an administration that campaigned on transparency and openness, the revelations today are very damaging."
An SNP spokesman said: “We thank Cllr Elder for his service to the SNP since he was elected to represent the Linn ward in 2012.
"We don’t recognise the characterisation of the group and it is unfortunate that his decision has come after a reshuffle.”