The utilization of high fidelity long read sequencing is critical for the resolution of repetitive genomes. Cannabis sativa is known to be diploid (2n=20), 70% repetitive, 64% AT rich and 1% polymorphic. The chemotypic genes (CBDAS, THCAS, CBCAS) governing cannabinoid synthesis are buried in multiple megabase LTR forests. High fidelity long read sequencers resolve these repetitive regions and enable genotypic classification of chemical expression. Pathogen resistance genes are equally important to the prediction of cannabinoid yield. Utilizing Pacific Biosciences HiFi sequencing, we construct reference grade genomes that enable population surveys of diverse chemotypes and pathogen resistant cultivars. We demonstrate the use of HiFi reads to resolve both complex medicinal plant genomes like Cannabis sativa L. and the rapid resolution of the medicinal fungal genome Psilocybe cubensis.