Concepts and methods were identified for their utility in evaluating the persistence and potential perturbations of genetically engineered microorganisms in the environment. Novel uses of DNA reassociation kinetics and gene probe technologies, in conjunction with conventional bacterial and plasmid isolation procedures, were found to provide the necessary sensitivity and specificity to detect genotypes in environmental samples. Detection of catabolic plasmid DNA, using a DNA:DNA colony hybridization approach, was achieved at a sensitivity of one target colony in one million nonhomologous background colonies. The methods were found useful for the rapid detection and isolation of specific catabolic microorganisms in environmental samples and were also valuable in monitoring genes in uncontaminated groundwater populations. Genetic methods can be used to provide insight into ecological processes that will affect the maintenance and effects of genetically engineered microorganisms or genes in the environment. (Copyright (c) 1987, Society for Industrial Microbiology.)