Rafting has long been invoked as a key marine dispersal mechanism, but biologists have thus far produced little genetic evidence to support this hypothesis. We hypothesise that coastal species associated with buoyant seaweeds should experience enhanced population connectivity due to rafting. In particular, invertebrates strongly associated with the buoyant bull-kelp Durvillaea antarctica might be expected to have lower levels of population genetic differentiation than taxa mainly exploiting non-buoyant substrates. We undertook a comparative genetic study of two co-distributed, congeneric chiton species, assessing population connectivity at scales of 61-516 km, using ≥186 polymorphic AFLP loci per species. Consistent with predictions, population genetic differentiation was weaker in the kelp-associated Sypharochiton sinclairi than in the rock-associated S. pelliserpentis. Additionally, while we found a significant positive correlation between genetic and oceanographic distances in both chiton species, the correlation was stronger in S. pelliserpentis (R2 = 0.28) than in S. sinclairi (R2 = 0.18). These data support the hypothesis that epifaunal taxa can experience enhanced population-genetic connectivity as a result of their rafting-ability.