Mnemiopsis leidyi A. Agassiz, 1865 is an invasive ctenophore that has spread to many areas of the Eurasian seas in recent decades and is one of the 100 most dangerous species in the world. This species was first observed in the northern Adriatic Sea in 2005 and then disappeared until 2016, when its first bloom was recorded. After that, it bloomed every summer in the area, causing severe damage to artisanal fisheries. Given the lack of genetic data for the northern Adriatic, here we compare the genetic diversity and phylogenetic relationships of M. leidyi populations sampled in 2016, 2018 and 2021 on the north-eastern coast of Italy with native populations and those introduced in other basins using two molecular markers: CytB and ITS. The CytB haplotype found in the samples from the northern Adriatic was identical to that found in the Gulf of Mexico and the Black Sea/Mediterranean. ITS analysis revealed 11 alleles, including 8 novel ones. The presence of a panmictic population in the northern Adriatic and the lower genetic variability compared to the native populations suggest that M. leidyi has been introduced into the Adriatic more than once and the species recently expanded in this area.