Salinity imposes a significant barrier to the distribution of many organisms, including diatoms. Diatoms are ancestrally marine, and the number of times they have independently colonized fresh waters and the physiological adaptations that facilitated these transitions remain outstanding questions in diatom evolution. The colonization of fresh waters by diatoms has been compared to "crossing the Rubicon," implying that successful colonization events are rare, irreversible, and lead to substantial species diversification. To test these hypotheses, we reconstructed the phylogeny of Thalassiosirales, a diatom lineage with high diversity in both marine and fresh waters. We collected approximately 5.3kb of DNA sequence data from the nuclear (SSU and partial LSU rDNA) and chloroplast genomes (psbC and rbcL) and reconstructed the phylogeny using parsimony and Bayesian methods. Alternative topology tests strongly reject all previous colonization hypotheses, including monophyly of the predominantly freshwater Stephanodiscaceae. Results showed at least three independent colonizations of fresh waters, and whereas previous accounts of freshwater-to-marine transitions have been discounted, these results provide compelling evidence for as many as three independent re-colonizations of the marine habitat, two of which led to speciation events. This study adds valuable phylogenetic context to previous debate about the nature of the salinity barrier in diatoms and provides compelling evidence that, at least for Thalassiosirales, the salinity barrier might be less formidable than previously thought.