Entity and instance determination, disambiguation, and referencing, referred to as authority control in libraries, are essential for scientific research. This study examines the authority control practices and issues in molecular biology using literature and scenario analyses. The analyses imply that the concept of authority control in molecular biology is associated with three tasks: named entity recognition, disambiguation, and unification. The identified authority control issues were conceptualized as quality problems caused by four sources: inconsistent or incomplete mapping, context changes, entity changes, and changes in entity metadata. This study can inform librarians and repository curators of the needs and issues of authority control in molecular biology and other related disciplines. © 2012 Authors.