Mr Bolton, who was elected party leader in September, tweeted to say Ms Marney had been suspended from the party "immediately upon us receiving this information".
According to the Mail on Sunday, Marney allegedly made a string of explosively racist remarks about Prince Harry's fiancée, claiming the black actress's entry into the Royal Family would "pave the way for a black king".
In a statement to the paper, Marney said she apologised "unreservedly" for the "shocking language" used in the messages, but said they had been taken out of context.
In the conversation, she also targets ethnic minorities in general, saying they are "pushing their way to the top slowly".
Marney sent the messages around three weeks before she entered a relationship with the current UKIP leader, the Mail On Sunday adds.
He is now facing calls to resign, with the party's National Executive Committee meeting on Thursday to decide his future.
The former Army officer left the mother of his two young children, 42-year-old Tatiana Smurova, for Ms Marney, whom he met shortly before Christmas. "And a black king". "In light of messages that have been brought to my attention, I have taken the decision to immediately suspend her party membership pending an investigation". The opinions I expressed were deliberately exaggerated in order to make a point and have, to an extent, been taken out of context.
He was responding to a teenage party activist who urged him to publicly call for Ms Marney to have her membership removed. Yet I fully recognise the offence they have caused.
"UKIP does not, has not and never will condone racism", he told the MoS. He was followed as leader by Diane James, who lasted just 18 days after feuding with the party's "old guard".