Arbuscular mycorrhizal (AM) cucumber seedlings and uncolonized controls were grown in growth chambers which allowed separation of compartments with roots from compartments with the extraradical mycelium alone. Two fungi, Glomus invermaium Hall and G. caledonium (Nicol. and Gerd.) Trappe and Gerdemann, were used. Bacterial numbers (direct and viable count) and activities (thymidine incorporation) were highest in the root compartment, but were not affected by the AM mycelium after 30 days of plant growth. The soil was stored after harvest for 16 d at 13°C to study the effect of disconnected mycorrhizal hyphae on bacterial activity. This treatment increased bacterial activity in mycorrhizal treatments compared to non-mycorrhizal control soils. The highest increase was found in the root compartment. The bacterial community structure was studied by analyzing the phospholipid fatty acid (PLFA) pattern. The bacteria specific PLFAs cy17:0 and cy19:0 increased in both experiments in the root compartments. The PLFAs 15:0 and 17:0, which are usually considered to be bacteria specific, also increased due to the presence of roots, but it was shown that these fatty acids were present in aseptically grown cucumber roots, and thus not bacteria specific. No bacterial PLFAs were affected by the presence of mycorrhiza.