Trevor Lowry was beaten by roadside
A Crown lawyer said a DNA profile matched the butt to 43-year-old James Speers, a self-employed businessman, from Ballyearl Close in New Mossley, County Antrim.
The accused, who was refused bail, denies the murder of Trevor Lowry, 49, in Glengormley, near Belfast, in March of last year.
Mr Lowry died in hospital two days after being beaten up while making his way home after a night out.
The court was told the cigarette butt was found under Mr Lowry's body.
It also contained component parts of Mr Lowry's DNA.
The lawyer said a forensic scientist had estimated the odds against the link being anyone else at one billion to one.
He said there was significant intelligence the accused was a leading member of the UDA.
Counsel for the accused said the matter was "eminently contestable" and his client wished to have it "tried as soon as possible as the charges are very tenuous".
Mr Speers also denies a charge of attempting to run over a man leaving St Enda's GAA club in Glengormley on the same night as Mr Lowry was attacked.