Microbes of the genus Methylobacterium are regularly associated with leaves and fruits of plants. In experimental tests, they promote the growth of germ-free liverworts and mosses, which are ancient land plants. In this study we analyzed the effect of M. mesophilicum, a bacterium that has been isolated from the organs of numerous plant species, including gymnosperms and angiosperms, on the development of sterile embryos of Ginkgo biloba L., a unique living fossil among the embryophyta. In addition, germ-free seeds of Pinus sylvestris were inoculated with the same strain of methylobacteria. In G. biloba seedlings that were raised in a 12 h dark/light regime, a promotion of root development was recorded in samples treated with the methylobacteria. A fresh mass increase of + 25 % occurred within 6 weeks of inoculation with bacteria, compared to the aseptic control. In contrast, shoot development of the same plants was not significantly affected by these bacteria. In Pinus seedlings, organ development was unaffected by the presence of methylobacteria. Our results document a differential sensitivity of the root system versus the shoot towards these ubiquitously distributed plant-associated bacteria. The data are discussed with reference to the isolated taxonomic position of Ginkgo biloba, one of the most primitive gymnosperms in the biosphere that is economically important as a medicinal plant