I want to have a popup div with iframe content.
Can search engines read this when I'm using jquery to create it?
Alternatively, is there a way to detect a search engine on the server side and remove the option of this popup?
The best way would be to degrade gracefully, e.g. by using a standard
<a id='mylink' href='xyz.html'>
link that points to the resource that is opened in the popup. You would then add the JQuery code to the link, causing it to open in the pop-up.
That way, even users that do not have JavaScript turned on can access your popup.
Most Lightbox clones like Thickbox work that way.