The pyrenoid structure of Trebouxia, a photobiont of two lichen species, Umbilicaria cinereorufescens (Schaer.) Frey and Parmelia sulcata Taylor, was investigated. In both lichen species, the pyrenoid of the photobiont exhibited straight, unbranched, long or short tubules. In the first lichen species, multiple pyrenoids were observed occasionally, while in the second one, homogeneous masses, called protein bodies, appeared between the thylakoids. These protein bodies were previously observed in some other species of the family Umbilicariaceae. Serial sections from single pyrenoids showed that tubules of the Impressa-type pyrenoid were closely associated with Pyrenoglobuli. The three-dimensional reconstruction of a complete chloroplast of a P. sulcata algal cell showed that the protein bodies were spatially separate structures. Immunolocalization techniques to detect the presence of ribulose-bisphosphate carboxylase (Rubisco) in the chloroplast showed that this enzyme was present primarily in the pyrenoid matrix. When protein bodies were present in the chloroplast, Rubisco appeared to be localized in these structures. The presence of pyrenoid satellites and protein bodies with reactivity to anti-Rubisco may be rebated to the nutritional conditions of the thalli.