Non-indigenous Daphnia ‘pulex’ have been found in many lakes in New Zealand (NZ) in the past 20 years, suggesting a recent invasion. However, very little is known about the origin of invasive D. ‘pulex’, whether they are D. pulex or D. pulicaria, and whether they are obligately asexual clones or cyclical parthenogens. Furthermore, the source and time of arrival of the invasive genotype(s) are unclear. We address these questions by genomic sequencing Daphnia populations from 13 lakes on the South Island and one on the North Island, NZ. Based on ~24,000 monomorphic species-specific markers, the invasive Daphnia on the South Island were found to be D. pulicaria, while those on the North Island are D. pulex/ pulicaria hybrids. Both the South and North Island Daphnia are phylogenetically clustered with North American D. pulicaria/pulex, thereby suggesting their North American origins. We further found that the South Island Daphnia populations are fixed heterozygotes for nearly all bi-allelic sites in the nuclear genome and contain identical mitochondrial genomes, suggesting the origin and proliferation from a single founder clone, which we experimentally verified to be an obligate asexual. Estimates from molecular data imply a colonization time for the South Island populations of ~ 60 years ago, with a likely invasion route associated with the introduction of salmonids from North America. Key words： Daphnia pulex; Daphnia pulicaria; invasion; obligately asexual; hybridization