Gibson Guitar Corp., a big user of ebony and other scarce woods, for years has allied itself with Greenpeace and other environmental groups to show it was serious about preserving forests.

That didn't stop the Nashville-based company, whose guitars are used by such musicians as B.B. King and Angus Young of AC/DC, from running afoul of U.S. authorities over allegedly illegal imports of wood. Though no charges have been filed, Gibson factories have been raided twice, most recently last week, by federal agents who say ebony exported...