The 6-deoxy sugar L-rhamnose (L-Rha) is found widely in plant and microbial polysaccharides and natural products. The importance of this and related compounds in host-pathogen interactions often means that L-Rha plays an essential role in many organisms. L-Rha is most commonly biosynthesized as the activated sugar-nucleotide uridine 5'-diphospho-ß-L-rhamnose (UDP-ß-L-Rha) or thymidine 5'-diphospho-ß-L-rhamnose (TDP-ß-L-Rha). Enzymes involved in the biosynthesis of these sugar nucleotides have been studied in some detail in bacteria and plants, but the activated form of L-Rha and the corresponding biosynthetic enzymes have yet to be explored in algae. Here, using sugar-nucleotide profiling in two representative algae, Euglena gracilis and the toxin-producing microalga Prymnesium parvum, we show that levels of UDP- and TDP-activated L-Rha differ significantly between these two algal species. Using bioinformatics and biochemical methods, we identified and characterized a fusion of the RmlC and RmlD proteins, two bacteria-like enzymes involved in TDP-ß-L-Rha biosynthesis, from P. parvum Using this new sequence and also others, we explored L-Rha biosynthesis among algae, finding that although most algae contain sequences orthologous to plant-like L-Rha biosynthesis machineries, instances of the RmlC-RmlD fusion protein identified here exist across the Haptophyta and Gymnodiniaceae families of microalgae. On the basis of these findings, we propose potential routes for the evolution of nucleoside diphosphate ß-L-Rha (NDP-ß-L-Rha) pathways among algae.