The population dynamics of a genetically engineered microorganism (GEM) in a microcosm was analysed using computer simulation models. The GEM Escherichia coli HB101/pBR325 was inoculated into the microcosm containing algae Chlorella vulgaris, bacteria Pseudomonas putida and protozoa Cyclidium glaucoma 14 days after cultivation of the microcosm was initiated. When the GEM was added at 10⁸cells·ml^-1 (high density), protozoa grew and then decreased rapidly. It recovered to the same population density as the protozoa in the microcosm without addition of the GEM. The GEM also rapidly decreased until it leveled out at the density about 10⁴cells·ml^-1 when protozoa increased. On the other hand, in the microcosm into which GEM was added at 10⁴cells·ml^-1 (low density), the population density of neither the indigenous bacteria nor the GEM changed. Based on empirical data, the differential equation which represents the indigenous bacteria and GEM population dynamics was developed and solved numerically. The simulation corresponded well with the empirical data. There was, however, a difference between high and low density introduction of the GEM in the values of parameter which represent theexchange of bacteria between the predated GEM by protozoa and non-predated GEM by protozoa. This indicated that the values of parameter changed when the GEM aggregated or when cell morphology of GEM occurred.