Botanical genomes contain abundant information, from which species-specific DNA regions can be pinpointed for use as markers. Molecular methods that can reliably access sufficient genomic data can serve as repeatable and definitive identification techniques. Through multiple case studies, we demonstrate how next generation sequencing (NGS) is a powerful tool allowing massive data generation and individual amplicon sequencing that can overcome conventional sequencing challenges: 1) Botanical blend products contain a variety of plant-based ingredients that require authentication. We developed primer sets for ~30 ingredients that can achieve species level identifications using one or more small genomic regions (≤150bp). Individual amplicon sequencing using NGS allowed for precise identification of target material, and detection of non-targets in some cases. NGS was exceptionally cost and resource efficient in high throughput runs (10+ samples) and was designed to be robust in identifying individual species within mixtures. 2) We further developed primer panels to identify individual mushrooms within multi-fungi ingredient matrices like Lion’s Mane, Chaga, Maitake, Shiitake, and Reishi. 3) Differentiating hybrid species from their pure parental counterparts can be difficult due to the extreme similarity of chemical and molecular markers. We developed a method that reliably delineates spearmint and peppermint specimens via targeted NGS of the multi-copy nuclear barcode region, ITS2. Observing a sequence composition that reveals a mix of two parent species effectively identifies a hybrid. In conclusion, the individual-amplicon sequencing ability of NGS allows for development of useful targeted tests that can be employed in a quality control environment.