The environmental Prototheca algae under certain condition are responsible for protothecosis infection in animal and human. The detail pathology and pathogenesis of this type of infection was unclear. Light microscopic diagnosis of Prototheca spp. algae is difficult with the use of routine histologic H&E stains. The specific stainsof fungusas periodic acid–Schiff (PAS) or Gomori Methenamine silver (GMS) were used and these stainsare not enough for examination of algae. A new modified staining method wasprepared. The main chemical constituents were Chromotrope2R, Aniline blueand phosphotungestic acid. The new stain gives very sharp affinity for staining of intra and extra cellular of Prototheca spp.microalgae and sporangium in different stages of maturation. The new stain will help the pathologist tostudy the pathology and pathogenesis of this type of pathogenic algae and considered the first specific stain for algae in tissue section.