Study of natural microbial ecosystems is hampered by our inability to closely duplicate the development of a community in the laboratory environment. The lack of such systems is particularly acute when endolithic microbes are examined. In this study, we have developed a system that enables laboratory growth of cryptoendolithic microbial communities resembling those found in the porous sandstones making up the Colorado Plateau in southeastern Utah. Microscopic examination of natural and in vitro cryptoendolithic biofilms shows that, on a gross level, the laboratory biofilm is developing in a fashion that is structurally similar to that of the native community. Further confirmation that the laboratory system resembles the native community was obtained by using denaturing gradient gel electrophoresis (DGGE) and DNA sequence analysis to examine the biofilms for the presence of cyanobacteria and the Geobacteriaceae. We found that the molecular profiles for these two groups of bacteria were nearly identical in the native and in vitro biofilms. These data show that our system for growing cryptoendolithic bacteria in the laboratory is suitable for the study of these ecosystems and will allow for experimental manipulations that are not possible in the field.