The first Japanese field trial testing the effects of genetically modified (GM) forest trees was conducted over a period of 4 years. Salt tolerance was conferred on Eucalyptus camaldulensis by introducing the soil microbe-derived choline oxidase (codA) gene into this plant. Three individual lines were planted in an isolated field owned by the Gene Research Center at the University of Tsukuba, following approval for type I use by the Ministry of Education, Culture, Sports, Science and Technology, Japan, and the Japanese Ministry of the Environment. Soil populations of fungi, actinomycetes, and bacteria fluctuated during sampling, but any differences introduced were observed only transiently, and no long-term change in the population was observed during the trial. Both the soil-mix as well as the sandwich method was employed to evaluate allelopathic activity of codA-transgenic E. camaldulensis. By the soil mix method, both GM and non GM-derived plant samples were found to exert negative allelopathic effects on seed germination, with an annual fluctuation. Overall, no significant differences were observed between the transformant lines and their bulk seed-derived non-transformants. The sandwich method also revealed an annual fluctuation. A comparison of the non-transformants and transformants revealed no significant differences in their allelopathic activity. Considering the practical use of these transgenic E. camaldulensis, they will no doubt be planted in some salinized sites. Thus, evaluating their impact on the ecosystem in saline conditioned fields might be important in the future.