Part of the Okta-AD Integration guide
If you imported an OU that contained AD Groups, those groups will now appear in Okta and cannot be deleted directly. To remove them, you need to deselect the OU from the import configuration and run a Full Import to clear them out.
Steps
In the Okta Admin Console, navigate to Directory → Directory Integrations and click the Active Directory integration.
On the Provisioning tab, under Settings, click Integration.
Clear the checkboxes for the OUs that contain the AD Groups you want to remove from Okta.
On the Import tab, click Import Now and select Full Import.
The unwanted groups will be removed from Okta after the Full Import completes.
Still having trouble? Create a support ticket and our team will be happy to help.