Technical Abstract: Histroically, Helicosporidium spp. were considered to be either protozoa or fungi, but have been unclassified since 1931. Recently, a Helicosporidium sp., isolated from the black fly Simulium jonesi Stone & Snoddy (Diptera: Simuliidae) has been amplified in the heterologous host Helicoverpa zea. Genomic DNA has been extracted from gradient purified cysts. The 18S, 26S, ,5.8S regions of the Helicosporidium ribosomal DNA, as well as some partial sequences of the actin and tubulin genes, were amplified by PCR and sequenced. Comparative analyses of these nucleotide sequences were performed using Neighbor-Joining and Maximum-Parsimony methods, and led to the construction of several phylogenetic trees that evaluated the position of Helicosporidium sp. within the phylogeny of eukaryotes. All trees depicted Helicosporidium sp. as a sister taxon to green algae (Chlorophyta), and this association was supported by significant bootstrap values. On the basis of this phylogenetic analysis, Helicosporidium sp.is clearly neither a protozoan nor a fungus, but appears to be the first described algal invertebrate pathogen. These conclusions lead us to propose the transfer of the genus Helicosporidium from Protozoa to Chlorophyta.