The paramecium bacterial endosymbiont Caedibacter taeniospiralis produces a protein R-body with four Reb subunits. Recently, a homolog of the gene responsible for the RebB subunit has been discovered as a trichocyst gene in the nuclear genome of a cryptomonad. Here we present our progress on developing a novel in situ methodology for detection of the RebB gene and a preliminary phylogenetic analysis of cryptomonad trichocysts genes found in freshwater and marine water samples.