Over the next five years, the two companies said, they will work on improving interoperability between their servers to improve systems management.
The pact calls for Microsoft to provide patent covenants for Xandros customers that ensure they are not infringing on Microsoft's intellectual property, according to the companies.
Xandros will also ship software for desktop productivity applications that translates between the Open Document Format and OpenXML, which is Microsoft's own document format.
The agreement will make it easier for Xandros customers to run a mix of Xandros and Microsoft software, Andreas Typaldos, CEO of Xandros, said in a statement.
Typaldos could not definitively say whether anticipated changes in the General Public License, which governs the distribution of Linux, will affect the terms of Xandros' partnership with Microsoft. The most recent draft of the GPL version 3 includes provisions to prevent patent-sharing agreements like the one between Microsoft and Linux vendor Novell.
"Xandros is fully aware of the development of the GPLv3 license. We will remain focused in our efforts to address our customers' interoperability and IP needs in a mixed source environment, and will remain flexible so we can adjust to future developments," Typaldos said in an e-mail.
Microsoft said the deal is part of its strategy to partner with open-source firms, including Novell and Zend Technologies.
Xandros is a Debian-based Linux distribution for desktops and business servers.