The species composition and extent of hybridization in Sparganium subgenus Xanthosparganium in North Eurasia reported in different published sources significantly vary. Thus, we aimed to clarify the taxonomy and distribution of aquatic Sparganium in that area. We supplemented the existing fragmentary genetic and morphological data mainly from North America and South Asia with our data from East Europe and North Asia. We combined molecular barcoding of the nuclear phyC and plastid psbJ-petA DNA regions (382 samples) with morphological analysis of herbarium collections (more than 1500 specimens from 16 herbaria) and numerous natural populations with a special focus on hardly accessible Siberian and the Far Eastern regions of Russia. We found that aquatic Sparganium is represented in North Eurasia by nine species and 14 hybrids. Nine previously unknown hybrids are formally described as new nothotaxa. All species and hybrids could be reliably discriminated with barcoding. We refined the distribution of all taxa in North Eurasia, e.g., S. angustifolium, a species avoiding continental areas, where it was confused by many authors with mostly vegetative specimens of other taxa. In the S. emersum complex in addition to recognized earlier widespread S. emersum and eastern North American S. chlorocarpum we proved the existence of one more distinct lineage – Asian Pacific S. rothertii. We discovered different evolutionary lineages within some species (e.g., S. glomeratum and S. hyperboreum) causing additional issues in the taxa identification. Almost all species cross with each other, usually acting both as plastid and pollen donors. Most of the hybrids are widespread and abundant. They originate each time when the ranges of parental species overlap and suitable habitats are available, and rather do not disperse from the centres of origin. Hybridization can be a threat to species with narrow ecological tolerance. Active gene flow is also evident within species when different evolutionary lineages come in contact (e.g., S. emersum, S. rothertii, S. glomeratum, S. hyperboreum, S. natans). We provide a new taxonomic treatment, which solves many long-standing issues in subgenus Xanthosparganium, and a new identification key for both species and hybrids occurring in North Eurasia.