The southeastern United States is a global biodiversity hotspot, meaning it is a center of endemism that is highly threatened by human activity. Much of this biodiversity is supported by a wide range of freshwater ecosystems. Freshwater aquatic ecosystems are also essential to a variety of economic services and ecological processes that humans rely on, but they are especially impacted by climate change and anthropogenic disturbance. Freshwater aquatic macrophytes form the foundation of food webs, remove excess nutrients and minerals from the water column, and serve as critical bioindicator species; they play a key role in maintaining community structure. However, aquatic plants, especially endemics, are understudied and under-collected, ultimately impeding conservation efforts. The pondweed family (Potamogetonaceae) is one of the most species-rich submersed aquatic plant families in the northern hemisphere. Pondweeds provide food, shelter, and habitat for organisms such as insects, fish, turtles, and waterfowl and can improve water quality. Potamogeton floridanus, the Florida pondweed, is a rare, endemic species currently known from few populations in the Blackwater River drainage in Florida. It has recently been suggested that P. floridanus is a hybrid between P. oakesianus and P. pulcher. Potamogeton species are known to readily hybridize, and it is estimated that there are more hybrids than distinct species in the genus. Hybrids may form a significant proportion of pondweed diversity in North America. However, hybrid species do not receive the same considerations for protection from policymakers and therefore, don’t receive necessary attention for conservation efforts. This study aims to (1) identify the factors contributing to the endemism of P. floridanus so that it may be better assessed for conservation, (2) develop a custom hybseq probe set for Potamogetonaceae to test its hybrid origin, and (3) advocate for better recognition of hybrid taxa in policy.