It is now well recognized that the increase in global transportation over the last two decades has brought with it an increased potential for the introduction of unwanted microorganisms (aquatic or terrestrial) that may have drastic effects on human and ecosystem health and agriculture. We have developed and validated a unique genetic fingerprinting tool for D. geminata. In concert, we developed field collection and preservation techniques specific for D. geminata along with genetic-based procedures that can now reliably detect D. geminate from a complex environmental community with a high degree of sensitivity. Recent work (Phase 2) has shown that the described methods will provide detection levels from <1 – 10,000 cells ml-1. We contend that the genetic based detection approaches used in this study offer great promise to meet the increasing demands to monitor the global threat from invasive micro-organisms.