It has come out that it is actually Apple that owns the Thunderbolt trademark, and not Intel.
According to MacNN, case filled with the US and Canadian trademark offices reveal that Apple is claiming the trademark, based on a filing it made in November 2010 in Jamaica.
As to why Apple and not Intel is filing for the Thunderbolt trademark despite being widely credited with its invention, no clear explanation has been forthcoming from either company to this moment.
It’s possible that if and when Intel’s technology is used in other companies’ products, it will be given a different name, leaving Thunderbolt name to be used by Apple exclusively. A quick search of U.S. and Canadian records have disclosed no awarding of such a trademark to Intel directly, raising the question of exactly how much of the technology was actually developed by Apple.