Gene probes hold a great promise as a tool in environmental sciences. They may be used to detect specific genotypes, to follow gene flow process, to delineate complex taxonomic aggregates and to monitor genetically engineered organisms in the environment. The sensitivity of the method is currently limited by experimental procedures and its specificity depends on the nature of the DNA sequences used as probes and the efficacy of lysing methods. Variable genetic determinants which code for the same trait determine the universality of gene probes. Finally, the method is highly feasible in terms of cost, speed and expertise. Current and future developments in molecular microbial ecology are likely to contribute toward the improvement of the probing methodology for the full realization of its potential in environmental sciences.