As demand for food increases, rapid testing methods are becoming increasingly important. In the past few years, yogurt has become popular. Yeast species are the most common spoilage organism, costing consumers and food companies money. A novel lateral flow assay has been developed to detect yeast oligonucleotide sequences. Gold nanoparticles were used as the standard reporter and fluorescent nanoparticles were developed as the novel reporter. The fluorescent nanoparticles were ruthenium-doped silica nanoparticles synthesized using the modified Stöber method. Visual analysis of assays using standard reporters showed the limit of detection to be 10 femtomoles of target sequence. Analysis of the fluorescent nanoparticles using a plate reader showed the limit of detection to be 0.027 femtomoles. The fluorescent reporter’s limit of detection is 1000 fold lower due to a sophisticated, more sensitive analysis method. Gold nanoparticles are appropriate for presence or absence testing, but fluorescent nanoparticles are best for obtaining quantitative data with low detection limits. Pathogens have been used as biological warfare for centuries. A brief review of common biowarfare agents is included. Yersinia pestis, the causative agent of the Plague, and Bacillus anthracis, the causative agent of Anthrax, are the focus. Additional work using gold nanoparticles as reporter in a sandwich assay is also included. The novel dye covered reporter was compared to the control, which was a single dye molecule linked to the reporter sequence. Repeated testing showed the novel reporter had a lower limit of detection and higher sensitivity due to increased ability to bind target.