Interactions between plants and microorganisms can significantly affect plant health and productivity as well as ecosystem functioning. Detailed knowledge of the tripartite relationships between plants, fungi, and bacteria, and their environment is still limited. In the present study, the soils adjacent to three plant species (Cruciata laevipes, Mentha piperita, Equisetum arvense) in the Ljubljana Marsh and the bulk, plant-free soil were analyzed for their bacterial community structure in June and October 2006. The terminal restriction fragment length polymorphism analysis indicated a different bacterial community structure in the rhizosphere and in bulk soil, however, with almost no seasonal changes between late spring and autumn samples and no apparent impact of the three plant species. In addition, root colonization of the three plant species by arbuscular mycorrhizal fungi (AMF) and dark septate endophytes (DSE) was microscopically assessed monthly from May until October 2006. A presumably accidental correlation between monthly precipitation and the degree of arbuscule formation, with the latter lagging 1 month, was noted for M. piperita, the most heavily colonized of the three plant species. With all three plants, the phosphorus content in roots correlated positively with most AMF structures. Microsclerotia of DSE were mainly abundant in autumn samples. Fungal diversity in roots was estimated using temporal temperature gradient gel electrophoresis separation of the fungal polymerase chain reaction products obtained for both 18S-rDNA and the 5.8S-ITS2-28S rDNA segments. No specific effects of either plant species or seasonal changes on mycorrhizal community structure were discernible.