Comparative phylogeography can inform many macroevolutionary questions, such as whether species diversification is limited by rates of geographic population differentiation. We examined the link between population genetic structure and species diversification in the fully aquatic sea snakes (Hydrophiinae) by comparing mitochondrial phylogeography in 16 species from two closely related clades that show contrasting diversification dynamics across northern Australia. Contrary to expectations from theory and several empirical studies, our results show that, at the geographic scale studied here, rates of population differentiation and speciation are not positively linked in sea snakes. The eight species sampled from the rapidly speciating Hydrophis clade have weak population differentiation that lacks geographic structure. In contrast, all eight sampled Aipysurus-Emydocephalus species show clear geographical patterns and many deep intraspecific splits, but have three-fold slower speciation rates. Alternative factors, such as ecological specialisation, species duration, and geographic range size, may underlie rapid speciation in sea snakes.