High throughput screening technology has allowed significant advances to be made in the discovery of lead agents for use in the pharmaceutical and agrichemical industries. However, economic and practical constraints have limited the use of this technology in the identification of bioactive microbes targeted at crop pests and diseases. Smaller scale targeted screening programmes have generally provided greater success in identifying microbial bioactivity. This paper describes a strategy for targeted selection of bioactive Trichoderma spp. Isolates are selected for biological characteristics that best match the biocontrol blueprint developed for the target pathogen and are then put through a series of standardised bioassays. This strategy provides a rapid and cost-effective means of identifying biocontrol agents with commercial potential.