Crested floating heart [Nymphoides cristata (Roxb.) Kuntze] is an invasive aquatic plant in the southeastern United States. For clonal plants like N. cristata, clonal diversity may influence response to control tactics and/or evolutionary potential. However, little is known about the diversity of introduced N. cristata. In this study, we used genotyping-by-sequencing to quantify N. cristata diversity in the southeastern U.S. and determine how that diversity is distributed across the invaded range. Our results show that at least three distinct genetic lineages of N. cristata are present in the southeastern U.S. Geographic distribution of the lineages varied, with one widespread lineage identified across several states and others only found in a single waterbody. There is also evidence of extensive asexual reproduction, with invaded waterbodies often host to a single genetic lineage. The genetic diversity reported in this study likely results from multiple introductions of N. cristata to the southeastern U.S. and should be considered by managers when assessing control tactics such as screening for biocontrol agents or herbicide testing. The extent and distribution of genetic diversity should also be considered by researchers studying the potential for invasive spread of N. cristata within the U.S. or hybridization with native Nymphoides species.