Aim We studied different species of gooseneck barnacles from the globally distributed rafting genus Lepas to examine whether the most widespread species are true cosmopolitans and to explore the factors influencing the phylogeny and biogeography of these epipelagic rafters. Methods We used a phylogenetic approach based on mitochondrial 16S and coI sequences, and the nuclear 18S gene to elucidate patterns of inter-and intra-species divergence. Altogether, five species of Lepas from 18 confined regions of the Atlantic, Pacific and Indic oceans were analyzed. Results A combination of nuclear and mitochondrial sequences provided robust phylogenetic signals for biogeographic classification of subgroups in Lepas species. Lepas australis, restricted to cold-temperate waters of the southern hemisphere shows two separate populations in the southern hemisphere (coastal Chile, other circum-Antarctic sampling sites) most probably related to temperature differences in the southern Pacific current systems. A more complex differentiation is seen for the cosmopolitan L. anatifera that thrives in warmer waters. In total, it is differentiated in four regional subgroups (coastal Chile, Oregon, Indopacific in general, Atlantic) and a global group, which might be either an ancient stemgroup, but more probably is an anthropogenic artefact. Separation into subgroups likely reflect geological vicariance effects. For Lepas, these were closure of the Isthmus of Panama, installation of the cool Benguela Current in the later Miocene including its persistence into the Present, Pleistocene current systems in the western Pacific differing from today, and in general lowered Pleistocene temperatures, and finally present-day current systems. The extreme ecological peer-reviewed) is the author/funder. All rights reserved. No reuse allowed without permission. generalists L. anserifera and L. pectinata are not differentated according to available data and might represent true global species. Data for L. testudinata remain ambiguous. Main conclusions Our data indicate cryptic speciation in some but not all species of the cosmopolitan epipelagic genus Lepas. Regional distribution of genetically different populations rely on a wealth of in part interacting inherited geological factors and modern traits. Controlling factors differ between species according to their ecospace limits and demonstrate the need for studies on species level to avoid unjustified generalizations. Data indicate that allopatric speciation is the main mode of divergence. True global species, if existent at all, need to be extreme ecological generalists, like Lepas pectinata and L. anserifera.