Abstract Forensic genetics is the application of genetics to human and nonhuman material for the resolution (and prevention) of legal conflicts. Nonhuman DNA applications are increasing, from the ancillary role in criminalistics to the control of protected species and their products, microbial identification in bioterrorism or medical malpractice. We review this growing applications’ scope and identify the major current difficulties, mainly resulting from the lack of standards and genetic databases as well as the poor or absent taxonomic definition of many major groups.