Here we describe how to use fluorescence in situ hybridization and immunofluorescence staining to determine the in situ distributions of specific mRNAs and proteins in Chlamydomonas reinhardtii. This unicellular eukaryotic green alga is a major model organism in cell biological research. Chlamydomonas is well suited for these approaches because one can determine the cytological location of fluorescence signals within a characteristic cellular anatomy relative to prominent cytological markers. Moreover, FISH and IF staining offer practical alternatives to techniques involving fluorescent proteins, which are difficult to express and detect in Chlamydomonas. The main goal of this review is to describe these powerful tools and to facilitate their routine use in Chlamydomonas research.