In March, 2000, shortly after the release of their Gift Horse album, Gene Eugene died.
In 2004, the band got together with Steve Hindalong to produce a special album for their summer tour. The result was entitled MUTT, and included new acoustic versions of ten songs originally written and recorded for each band member's regular rock bands. The following year, the band would release the almost entirely instrumental Island Dreams. The Lost Cabin and the Mystery Trees, was released July 2006.
In 2008, the Lost Dogs traveled down historic Route 66 with cinematographer Jimmy Abegg. Abegg filmed the band's experiences. The band then wrote and recorded 14 songs inspired by their journey, which was released as Old Angel in May 2010.