Mass culture of oleaginous microalgae in open raceway ponds is considered to be the cost-effective method for biodiesel production. The oleaginous green alga Graesiella sp. WBG-1 is an industrial strain capable of high lipid productivity, but it is subject to parasitism. In the present study, an epibiotic parasite EPG01 was found in cultures of the oleaginous Graesiella sp. WBG-1 and had devastating effects on microalgal growth and lipid accumulation in open raceway ponds. Based on analyses of the morphology, ultrastructure, 18S rDNA-based phylogeny, and host specificity, the parasite EPG01 was identified as Rhizophydium scenedesmi. Moreover, the host specificity test showed that only three coccoid green algae strains were rapidly and intensively infected by the parasite EPG01: Chlorococcum sp. A213, Chlorococcum sp. GP1, and Graesiella sp. WBG-1. This is the first documented report of R. scenedesmi infection in oleaginous coccoid green algae. This present study verified the presence of haustorium and the thick-walled resting sporangium and also proposed a life cycle description for R. scenedesmi. Our results will improve understanding of parasite-host relationships and help to establish strategies for the control of parasitic contaminations.