XPath and Namespaces
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Essentially, you have to just make one up, and use it in your query. For example, if the root element is /foo, you need to search for /prefix:foo, where "prefix" is the namespace prefix you invent.
XPath and Default Namespace handling talks about how to do this. I found this document useful, although my JDOM code ended up being a bit simpler than the example given.