Following Sun Ra's death, the Arkestra was led by tenor saxophonist John Gilmore. Following Gilmore's death in 1995, the group has performed under the direction of alto saxophonist Marshall Allen. A 1999 album led by Allen, Song for the Sun, featured Jimmy Hopps and Dick Griffin. In the summer of 2004 the Arkestra became the first American jazz band to perform in Tuva, in southern Siberia, where they played five sets at the Ustuu-Huree Festival.
As of May 2008, the Arkestra continues to tour and perform. In September 2008 they played for 7 days in a row at the ZXZW festival, each day emphasizing different aspects of the musical legacy of Sun Ra. In 2009, they performed at Philadelphia's Institute of Contemporary Art in conjunction with an exhibition that explored the intersection of the Arkestra's performing legacy and the practice of contemporary art. More recently they ventured to Australia for the first time, for the 2011 Melbourne International Jazz Festival and MONA (Museum of Old and New Art) in Tasmania.