Abstract The ctenophore Mnemiopsis leidyi is native to the Atlantic coasts of the Americas and is considered a threat to biodiversity and food webs in recipient ecosystems. Most of these invasive ctenophores perish during the cold winter in temperate northern European waters (North and Baltic Seas) but spread again every summer/autumn. We collected ctenophores from the southern North Sea, inner Danish waters, and western Baltic Sea in 2017 and 2018, and sequenced genomic DNA obtained from tissue samples. We obtained sequences of internal transcribed spacer (ITS) 1 and 2, and the intervening 5.8S fragment and partial fragments of the flanking 18S rRNA and 28S rRNA genes from nuclear DNA. Excluding the rRNA regions and focussing on only the two ITS sequences, we compared with ITS sequences archived in databases from specimens in its native (Northwest Atlantic) and other invaded habitats (Caspian Sea, Mediterranean Sea, central-western Atlantic Ocean). The comparison revealed no significant difference in genetic variation among temperate northern European sampling locations but showed variation when compared with native and other invaded habitats. No significant genetic difference was identified between specimens collected in the temperate northern European waters for two consecutive years. The very low interregional and interannual genetic variations in M. leidyi specimens in the Northeast Atlantic are consistent with the presence of one single panmictic population in northern European waters and with the hypothesis, also suggested in previous studies, that annual dispersal from the southeastern North Sea into the western Baltic Sea can be traced back to the same population, which most likely originates every spring from the Dutch Wadden Sea and the English Channel.