The Shepherd Project is a software framework to support capture-mark-recapture (CMR) studies. CMR is a core technique used in the analysis and management of wildlife populations. The Shepherd Project promotes non-invasive "virtual tagging" mark-recapture techniques (e.g., photo-identification via natural coat/skin coloration instead of physical tags attached to animals) to protect both animals and researchers in population studies. The aim of the Shepherd Project is to aid researchers in obtaining and managing CMR data to better understand and manage animal populations. The Shepherd Project is most successfully used as a collaborative, public-facing Web site, allowing members of the research community to collaborate and analyze data "behind the scenes" (with login access) and allowing members of the public to collect data as "citizen scientists" and submit it through submission forms.