Bioluminescence in dinoflagellates is controlled by HV 1 proton channels. Database searches of dinoflagellate transcriptomes and genomes yielded hits with sequence features diagnostic of all confirmed HV 1, and show that HV 1 is widely distributed in the dinoflagellate phylogeny including the basal species Oxyrrhis marina. Multiple sequence alignments followed by phylogenetic analysis revealed three major subfamilies of HV 1 that do not correlate with presence of theca, autotrophy, geographic location, or bioluminescence. These data suggest that most dinoflagellates express a HV 1 which has a function separate from bioluminescence. Sequence evidence also suggests that dinoflagellates can contain more than one HV 1 gene.