Nicola Sturgeon had initially backed his decision to stay on as an MSP in the party group after he stood down as a minister a fortnight ago.
This was believed to be down to inappropriate comments in a text.
But a spokesman for the SNP said tonight: "Following new information being received by the SNP over the course of the last 24 hours relating to the behaviour of Mark McDonald, he has been suspended from both the parliamentary group and the party while further investigation takes place.
"In the interests of due process and appropriate confidentiality no further comment will be made.”
Mr McDonald had said today it would be down to his constituents to decide on his future as an MSP, before tonight's decision was taken.