As ancestors of higher plants, mosses offer advantages as simple model organisms in studying complex processes. The moss Physcomitrella patens became a powerful model system in the last few years (Cove and Knight, 1993). Adaptation of PEG-mediated DNA uptake procedure has permitted the establishment of efficient molecular genetic approaches. To study possible effects of a Type I phytochrome, the potato phyA gene was introduced into the moss P. patens. Stabile transformants exhibited a range of similar phenotypes (Schaefer et al., 1991). The aim was to differentiate the wild type from the transgenic moss plants with simple, quick measurements providing data suitable for analyzing offspring populations. Ten different morphological and biochemical methods were used to investigate the phenotype in order to choose the best phenotypical category to indicate the presence and the effect of the phytochrome transgene. Two selected strains were used with the most and the least intensive phenotypical features (3*, 29), along with their selfed progenies, as well as progenies from crosses with the nicotinic-acid auxotrophic mutant. The best methods to differentiate between wild type and transgenic plants were the statistical analysis of the number of gametophores, photometric measurement of pigment contents and composition under different light conditions, color evaluation by PC-based vision system, and visual observation of morphogenetic changes. Our investigations support that the potato phytochrome transgene has a pleiotropic effect in the moss P patens. The methods used would be applicable for the characterization of mosses with different transgenes.