Many studies have highlighted the broad utility of herbaria in plant evolutionary biology by analyzing DNA obtained from specimens of variable ages. However, the breadth of species found in herbaria presents issues regarding methods used for molecular studies, including DNA isolation. Some species may preserve better than others, while others may produce significant secondary compounds that inhibit DNA isolations. The Hawaiian Plant DNA Library presents a unique opportunity to investigate the quality of DNA in herbarium specimens compared to long-term freezer storage. For decades, herbarium specimens of Hawaiian endemic species have been paired with a contemporary DNA extraction (i.e., herbarium sheet made in 1995 and DNA extraction performed in 1995), which has been stored in a freezer. We have used this unique collection to compare how herbarium sheet DNA and their frozen isolated DNA counterparts perform in high-throughoput sequencing for speices in 12 genera of Hawaiian plants. By assembling chloroplast genomes, as well as mapping reads to Angiosperm 353 genes, we sought to quantify the effects of herbarium storage of tissue vs. freezer storage of isolated DNA. Herbarium samples were statistically more fragmented and produced fewer complete circular chloroplast genomes compared to their freezer stored DNA counterparts. However, there were numerous species-specific instances of herbarium samples performing exceptionally well. Overall, this study highlights the importance of obtaining high quality DNA at the time of vouchering a plant for herbarium storage. This is especially important in areas of the world with high concentrations of endemic and/or threatened taxa, such as Hawaiʻi.