Horizontal gene transfer (HGT) is an important and potentially frequent process impacting the evolutionary trajectory of eukaryotic species. Yet to date, the mechanism of HGT among eukaryotes has remained a mystery. Here, we demonstrate that Starships, a newly discovered group of cargo-mobilizing transposable elements, are active vectors of horizontally transferred DNA among eukaryotic species. We find that multiple Starships simultaneously transfer themselves and their cargo within and between fungal genera separated by upwards of 100 million years of evolution. Transferred Starships are recovered in strains with and without selection for particular Starship-encoded phenotypes. Using whole genome sequencing, we exclude alternative hypotheses such as heterokaryosis, parasex or the random uptake of exogenous DNA by showing that only Starship DNA is precisely transferred. Furthermore, we demonstrate that the introduction of the Hephaestus Starship into a new species increases metal resistance due to the genes carried by this element. Between 18-27% of all Starships in our focal genus, Paecilomyces, have evidence of horizontal transfer under natural conditions, including to other fungal genera, revealing Starship-mediated HGT to be a widespread and frequent phenomenon across filamentous fungi. This study identifies the first active genetic mechanism for HGT between eukaryotic species.Competing Interest StatementThe authors have declared no competing interest.