Collections of Colonies of Bees was started as a side project for Chris Rosenau and Jon Mueller, both of the post-rock group Pele. In 1998, they formed the group as an outlet to explore traditional folk/bluegrass instrumentation routed through modern electronics. In 2003, the group began its steady procurement of members, enlisting Jon Minor. The following year, the group signed to Polyvinyl Records and added a fourth member, Jim Schoenecker. In 2006, the Bees reconstituted itself as a powerhouse live group, adding Thomas Wincek and Daniel Spack.
The group went through further lineup changes after several members (Mueller and Wincek) left to form Volcano Choir with Justin Vernon of Bon Iver. In 2011, a revamped lineup released the album "Giving" on the Hometapes label.