Rafting on floating seaweeds facilitates dispersal of associated organisms, but there is little information on how rafting affects the genetic structure of epiphytic seaweeds. Previous studies indicate a high presence of seaweeds from the genus Gelidium attached to floating bull kelp Durvillaea antarctica (Chamisso) Hariot. Herein, we analyzed the phylogeographic patterns of Gelidium lingulatum (Kützing 1868) and G. rex (Santelices and Abbott 1985), species that are partially co-distributed along the Chilean coast (28°S–42°S). A total of 319 individuals from G. lingulatum and 179 from G. rex (20 and 11 benthic localities, respectively) were characterized using a mitochondrial marker (COI) and, for a subset, using a chloroplastic marker (rbcL). Gelidium lingulatum had higher genetic diversity, but its genetic structure did not follow a clear geographic pattern, while G. rex had less genetic diversity with a shallow genetic structure and a phylogeographic break coinciding with the phylogeographic discontinuity described for this region (29°S–33°S). In G. lingulatum, no isolation-by-distance was observed, in contrast to G. rex. The phylogeographic pattern of G. lingulatum could be explained mainly by rafting dispersal as an epiphyte of D. antarctica, although other mechanisms cannot be completely ruled out (e.g., human-mediated dispersal). The contrasting pattern observed in G. rex could be attributed to other factors such as intertidal distribution (i.e., G. rex occurs in the lower zone compared to G. lingulatum) or differential efficiency of recruitment after long-distance dispersal. This study indicates that rafting dispersal, in conjunction with the intertidal distribution, can modulate the phylogeographic patterns of seaweeds.