Mr Bolton, 54, was already facing calls for his resignation after he left his wife for 25-year-old Jo Marney.
Party chairman Paul Oakden told the Mail on Sunday that Ms Marney was suspended from the party membership immediately after he was made aware of the messages.
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She also described Markel as a "negro" and said that black people were ugly.
Speaking of minority groups in general, she claimed they were "pushing their way to the top slowly. Next will be a Muslim PM and a black king".
In a letter to members, Oakden said the party's national executive committee ruling body agreed to discuss the leader's private life at a special meeting in January.
A Ukip spokesman said Ms Marney had been suspended from the party. "And a black king".
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Asked whether the allegation was one of racist abuse, Pardew added: "I don't know, it's been directed straight to the referee". There was a stoppage in play while the referee spoke to his fourth official before he allowed play to continue.
If he is ousted then the party will have to elect its fifth leader in just 18 months. "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".
On Sunday, he dismissed claims on Twitter that he was in Ms Marney's company when he appeared on television in mid-October as "rubbish".
On her Twitter profile, Marney describes herself as a model, actor and journalist, as well as a Brexiteer. The opinions I expressed were deliberately exaggerated in order to make a point and have, to an extent, been taken out of context. "Yet I fully recognized the offense they have caused", she said.
"Also it would be hypocritical to allow her to stay. because he said in the leadership election he was the candidate against racism and nazis so she has to go or he and UKIP are doomed if we let this behaviour happen in the party". Bolton's may also be suspended from Ukip following a series of investigations. Photo taken by Gawain Towler (Ukip communications official).
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