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Field observations of morphologically intermediate water lilies in central Canada suggested a hybrid origin involving the parents Nymphaea odorata Aiton and Nymphaea leibergii Morong despite the fertile nature of these plants. Sequencing of the nrITS and the plastid rps4–trnT–trnF regions further including all members of the north temperate Nymphaea subg. Nymphaea clade, and samples from other hybrids occurring in North America in the wild, allowed us to determine that individuals of N. leibergii and of N. odorata were the maternal and paternal parents, respectively. Hybrids of New England have all proven to be sterile, are genetically variable, and probably are F1. By comparison, the plants of east-central Saskatchewan and west-central Manitoba are fully fertile and genetically uniform based on ISSR and sequence data. On the basis of this evidence, the latter are here described as a new species, Nymphaea loriana sp. nov., which may have originated during the Holocene climatic optimum about 6000 years ago in a past contact zone of the parents. Further hybrids detected between N. odorata and Nymphaea tetragona Georgi, as well as between N. leibergii and N. tetragona, were always sterile. Gene trees of the temperate clade of Nymphaea converge on a clade of small-flowered water lilies (sect. Chamaenymphaea), including N. leibergii, N. tetragona, and Nymphaea pygmaea. Nuclear ITS further resolves an American clade (Nymphaea mexicana Zucc. – N. odorata) sister to all remaining species. This split into two major subclades also appears in the otherwise less resolved rps4–trnT–trnF tree. Thus the origin of N. loriana is a reticulation between long-separated parental lineages.