Bryophytes have been powerful experimental tools for the elucidation of complex biological processes. Analysis of organisms from these ancient clades is an active and ongoing enterprise that will provide greater insight into the development, physiology, phylogenetics, and stress-induced cellular responses of plants. To maintain their relevance as experimental models, the analysis of mosses must expand to include modern molecular tools such as a knowledge of the genome via large-scale DNA sequencing, the ability to create transgenic individuals via transformation, and the capability to create gene knock-outs by homologous recombination. The availability of these molecular tools is limited when compared to flowering plants. However, in mosses such as Physcomitrella patens, Funaria hygrometrica, Ceratodon purpureus, and Tortula ruralis these tools are rapidly being developed for the study of molecular genetics. Efficient targeted gene disruption (i.e., homologous recombination) is a well-established tool in both yeast and murine cells that until recently was unknown in any plant model system. Recently, Schaefer and Zryd (1997) demonstrated that efficient homologous recombination occurs in P. patens. The ability to perform efficient homologous recombination in P. patens is at present unique amongst all plants and represents an extremely powerful technique for the functional analysis of plant genes.