Soil-borne diseases such as Armillaria root rot and facial eczema in ruminants costs our economy $100’s millions annually, and the inability to predict future outbreaks represents a substantial biosecurity risk. Our extensive library of DNA samples provides substantial opportunities allowing us to probe for the presence of key pathogenic taxa across New Zealand’s varied land uses. The analysis of soil bacterial and fungal DNA can allow us to identify taxa identified as being of significant interest to NZ primary industries. These may include the causative agents of Armillaria root rot disease in plantation forest, facial eczema in ruminants, and major diseases of cereal/horticultural crops (e.g., Botryosphaeria dieback). In addition to mapping the distribution of these organisms across NZ soils and land use types, comparison of soil microbial data with soil physico-chemical attributes can allow us to predict soil factors that may suppress or benefit each pathogen under investigation.