The Helicosporidia are a unique group of pathogens found in diverse invertebrate hosts. They have been considered to be either protozoa or fungi, but have remained incertae sedis since 1931. Following the isolation of a Helicosporidium sp. in Florida, we showed that the Helicosporidia are non-photosynthetic green algae. Phylogeny reconstruction inferred on several housekeeping genes (including actin and b-tubulin) consistently and stably grouped Helicosporidium sp. among member of Chlorophyta. Additionally, nuclear SSU rDNA phylogenies identified Helicosporidium as a sister taxa to another parasitic, non-photosynthetic algal genus: Prototheca (Chlorophyta, Trebouxiophyceae). Comparison of mitochondrial (cox3) and chloroplast (rrn16) genes confirmed that Helicosporidium and Prototheca have arisen from a common photosynthetic ancestor, and suggested that Helicosporidia contain Prototheca-like organelles, including a vestigial chloroplast (plastid). In an effort to better characterize the biology of Helicosporidium sp., a cDNA library has been constructed and expressed sequences tags (ESTs) have been generated. Most of these ESTs exhibited similarity with algal and plant genes. Significantly, the EST library provided with additional evidence that Helicosporidium sp. does have a plastid, as numerous nuclear-encoded, plastid-targeted genes were identified. Characterization of the plastid is currently underway: several chloroplast-like genes (rrn16, rrn23, tufA) have been cloned and their sequences are being used to isolate the entire plastid genome. Similar to the situation described in Prototheca, the Helicosporidium plastid may be reduced, as most of the genes involved in photosynthesis likely have been lost during the course of evolution.