Hydrocotyle (water-pennywort) is a genus of aquatic and wetland herbaceous plants, comprising 180 species worldwide. In North America, there are only four native Hydrocotyle species and four non-native species, yet not every species is represented by comparable DNA sequence data. The absence of DNA sequences for some species has prevented them from being included in a comprehensive phylogeny for the genus. Moreover, unknown plants cannot be identified using DNA sequences if there is not a suitable comparison sequence available for every species. We set out to obtain DNA sequences for species that had not been sequenced before and to make sense of existing sequences that may have been misidentified. During the process of evaluating DNA sequences, we learned that about one-tenth of previously published sequences had been misidentified, sometimes even to the wrong plant genus or family. We obtained the first DNA sequence data for H. moschata, which is native to New Zealand and adventive in California. We also clarified the names and genetic distinctness of two other native species, H. umbellata and H. verticillata. Two kinds of interspecific hybrids are reported: H. umbellata × H. verticillata, identified in cultivated plants, and H. bonariensis × H. umbellata from Georgia, USA. Several native North American species resolved in a clade along with the Palearctic H. vulgaris, and the closest relatives are native to Europe and South America. This study has produced the most complete phylogenetic understanding of Hydrocotyle to date.