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Simple Summary: The genus Craspedacusta comprises invasive freshwater jellyfish species present in all continents except Antarctica. Due to the morphological plasticity of the medusa stage, the number of species in the genus Craspedacusta is still disputed. Here, we shed new light on the distribution of the genetic lineages of these non-native species across the Italian peninsula, Sicily, and Sardinia. Since the first Italian record in 1946 and up to the last available review in 2017, Craspedacusta medusae were reported in 40 Italian water bodies. In the present study, we report 21 new records of Craspedacusta medusae presence since its latest finding in 2017. Furthermore, we present results of the molecular analyses conducted on the collected medusae. Our findings show the presence of two distinctive genetic lineages of Craspedacusta in Italy: (i) a group whose distribution ranges from central to northern Italy; and (ii) a group that comprises three populations from northern Italy and the single Sicilian population known to date. Olindiid freshwater jellyfishes of the genus Craspedacusta Lankester, 1880 are native to eastern Asia; however, some species within the genus have been introduced worldwide and are nowadays present in all continents except Antarctica. To date, there is no consensus regarding the taxonomy within the genus Craspedacusta due to the morphological plasticity of the medusa stages. The species Craspedacusta sowerbii Lankester, 1880 was first recorded in Italy in 1946, and until 2017, sightings of the jellyfish Craspedacusta were reported for 40 water bodies. Here, we shed new light on the presence of the freshwater jellyfishes belonging to the genus Craspedacusta across the Italian peninsula, Sardinia, and Sicily. First, we report 21 new observations of this non-native taxon, of which eighteen refer to medusae sightings, two to environmental DNA sequencing, and one to the finding of polyps. Then, we investigate the molecular diversity of collected Craspedacusta specimens, using a Bayesian analysis of sequences of the mitochondrial gene encoding for Cytochrome c Oxidase Subunit I (mtDNA COI). Our molecular analysis shows the presence of two distinctive genetic lineages: (i) a group that comprises sequences obtained from populations ranging from central to northern Italy; (ii) a group that comprises three populations from northern Italy—i.e., those from the Lake Levico, the Lake Santo of Monte Terlago, and the Lake Endine—and the single known Sicilian population. We also report for the first time a mtDNA COI sequence obtained from a Craspedacusta medusa collected in Spain. [ABSTRACT FROM AUTHOR]