Gene targeting is a highly effective and straightforward technique for the functional analysis of a gene of interest. However, its efficiency is not satisfactorily high in many model plants including Arabidopsis thaliana. In the moss Physcomitrella patens, a model species of basal plants, the efficiency of gene targeting is as high as in yeasts, and this moss is becoming widely recognized as an experimental model of choice in various areas of plant biology. Here we focus on the transformation of protoplast cells and on the measurement of bioluminescence rhythms from protonema tissues of luciferase reporter strains in P. patens, both of which are important for mechanistic studies of the circadian clock.