Diseases and biological toxins have been used as weapons of war throughout recorded history, from Biblical times through to the present day. Bioweapon uses have historically been directed primarily, although not exclusively, against human populations. Specialised technicians and state-of-the-art research facilities are no longer necessary for the production or deployment of many known bioweapon agents and commercially available technologies now permit the large-scale production of bioweapon agents in small-scale facilities at relatively low cost. Failures in the detection and containment of bioweapon and emerging disease outbreaks among populations of wildlife and indigenous peoples in developing countries could result in severe erosion of genetic diversity in local and regional populations of both wild and domestic animals, the extinction of endangered species and the extirpation of indigenous peoples and their cultures. Our ability to understand and control the spread of diseases within and among human and animal populations is increasing but is still insufficient to counter the threats presented by existing bioweapon diseases and the growing number of highly pathogenic emergent infections. Interdisciplinary and international efforts to increase the monitoring, surveillance, identification and reporting of disease agents and to better understand the potential dynamics of disease transmission within human and animal populations in both industrialised and developing country settings will greatly enhance our ability to combat the effects of bioweapons and emerging diseases on biological communities and biodiversity.