As we continue to document the diversity of epizoic diatoms, we can channel greater effort into understanding the nature of the interaction between the diatoms and their host organisms. Among diatoms, the genus Achnanthes Bory is unique in that it contains taxa which grow opportunistically on both epizoic and non-epizoic benthic habitats as well as taxa which are restricted to epizoic habitats. One of these latter taxa, Achnanthes elongata, stands out as a more ecologically flexible species, having been documented on a variety of marine vertebrates, including manatees, diamondback terrapins and four species of sea turtles. We isolated, cultured and documented morphology and DNA data from Achnanthes cells from manatees, dolphins, sea turtles, terrapins and sea snakes from multiple locations on both sides of the Atlantic Ocean and from the Indian Ocean. Molecular phylogenetic inference of the DNA sequence data from these strains implied a single transition to an exclusively epizoic habitat (in Achnanthes elongata and Achnanthes squaliformis) but could not resolve any fine population-level patterns regarding host specificity or biogeography. We also take the opportunity here to describe a novel taxon of Achnanthes, Achnanthes angustelliptica sp. nov., which was collected from a manatee but has been documented in other habitats as well.