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I'm having a hard time understanding the purpose of adding an SPGroup to the AssociatedGroups collection (or its respective property bag item) of a site other than the group(s) appearing in the quick launch.

This confusion does not apply to the Associated[Visitor|Member|Owner]Group property; those are clear.

What other purpose(s), if any, do these associated groups provide? Is this another way to define roles at the site level when breaking inheritance?

Thank you.

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Groups return all groups which have security roles assigned to the current site.

AssociatedGroups return all groups visible in the left menu of the People and Group page. Those groups may not have access to the current site (if the security settings do not inherit from parent site). In this case, some of them will not be listed in the Groups property.

To view the difference, in a subsite, create a new group without giving any permission. The group will be visible in the AssociatedGroups and Left menu, but will not be listed in Groups or Site Permissions page.

Reference: The accepted answer on the question SPWeb.Groups vs. SPWeb.AssociatedGroups

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...in addition to Benny's - the associated groups are also used to "link" a sub-site security to a certain SP-group. That is also because groups, as permissions levels as ONLY stored at the site collection level.

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