The Natural Health Product (NHP) market has been on an upward trajectory in growth over the past several years. Unfortunately, a parallel trend has been observed with increased cases of fraud, driven by economically motivated efforts to adulterate with off-label ingredients. Fraud can happen at any stage of the supply chain; thus, accountability of authenticity lies with every manufacturer. Unfortunately, minimal requirements exist for product testing, with finished product manufactures being responsible for conducting one scientifically valid test to determine quality. This line of defense should ensure consumer confidence, financially and health-wise. That confidence is threatened when quality control programs do not address all relevant fraud vulnerabilities. Molecular authentication techniques are a recent venture in NHP quality testing, with analytical chemistry being the conventional practice. These DNA- based techniques bring value in their superior ability to make direct taxonomic identifications of ingredients. The greatest concern around these methods is uncertainty around the presence of DNA analyte in processed products, due to degradation. Until now, a lack of empirical investigation into this concept has fueled skepticism about the application of molecular methods to processed NHPs. I sought to document the dynamics of DNA quality and quantity through production of a highly processed green tea extract. I observed degradation and removal of DNA, but also remainder of sufficiently intact and abundant DNA for identification. This finding encouraged an exploration of molecular authentication application in other highly processed botanical products, namely, plant-based protein powders. Conventional protein powder quality control pipelines are lacking and in need of alternative methods. I demonstrated success of two DNA-based techniques — polymerase chain reaction and next- generation sequencing — and compared them to an advanced analytical chemical method (LC-MS/MS). Success begged the question: can molecular techniques be used for more than identification? Next, I designed and validated a multiplex qPCR assay to detect and quantify pea and soy DNA in mixtures. Good quantitative linearity suggested applicability of this tool to industry and highlighted important considerations for implementation. This thesis serves as a demonstration of the utility of molecular techniques in NHP authentication, and justification for investigation of application with all processed botanicals.