The angiosperm genus Myriophyllum (Haloragaceae) is among the most species-rich genera of aquatic core-eudicots. Myriophyllum has a cosmopolitan distribution with its center of diversity in Australia (> 37 endemics). The widespread invasive species of the genus (M. aquaticum, M. heterophyllum, and M. spicatum) have drawn attention from international natural resource managers. Myriophyllum species are notoriously difficult to identify using vegetative morphology alone, which commonly is all that is available for these highly clonal plants. The relationships among taxa have been difficult to determine with suspected parallelisms in sex expression, sepal and petal loss, and reduced stamen number. A molecular phylogenetic approach was taken to examine relationships among taxa and to employ molecular markers for the reliable identification of Myriophyllum species. This study included ≈ 80% of the known Myriophyllum species. Both nrDNA ITS and cpDNA matK and trnK data were used to examine phylogenetic relationships among species. The nrDNA ITS data proved highly variable and could differentiate between all but one species pair examined. These analyses also uncovered multiple cryptic species among Australian complexes. Phylogenetic results support major realignments in the subgeneric classification including a recombination for the rare monotypic genus Meziella, which was nested within Myriophyllum. Here we present the new combinations and taxa Myriophyllum subgenus Meziella, sections Pectinatum and Pelonastes, subsections lsophylleae and Nudiflorum with the new combination Myriophyllum trifidum to accommodate the former monospecific genus Meziella.