Phylogeographic relationships were inferred from nuclear rDNA internal transcribed spacer (ITS) sequences among ten biogeographic isolates of the cosmopolitan green alga Cladophora vagabunda from the Atlantic and Pacific Oceans as well as the Red Sea and SW Australia. Representatives of the closely related C. albida/sericea clade were used as outgroup and root, based on previous studies using 18S rDNA. High bootstrap values and negative g1-statistics revealed a strong phylogenetic signal regardless of assumption sets that included or excluded alignment-gaps in the analyses. The two main lineage found within the C. vagabunda complex are hypothesised to have shared a common Pacific ancestor, based on the basal position of Indo-West Pacific isolates relative to the outgroup. It is concluded that C. vagabunda represents the predicted intermediate case between ancient tropical species that exhibit strong vicariance imprints and recent, cold-temperate to boreal lineages that do not.