Arbuscular mycorrhizal fungi (AMF) may have a major role in phosphorus nutrition of crops in Lombok, where fertilizer use is low. As a start to understanding this role, AMF dynamics were monitored from the 1999 non-rice season to the end of the 1999/2000 rice season at 32 sites including dryland systems with no rice, upland rice and flooded systems with one or two rice crops per year in the rotation. Over all four systems, root colonization was greater in vertisol (22.3 % of roots) than in regosol (9.5 %) soil, possibly due to lower Bray-1 P content of the vertisol (6.2 v. 13.7 mg kg−1). Colonization was poor in flooded rice (3.1–5.1 %); at the same sampling times it was better in upland rice (10.6–13.4 %) and in non-rice crops growing in dryland systems (13.8–17.0 %). Therefore, the low colonization in flooded rice appeared to be the result of flooding, rather than the rice itself. Flooding also reduced transparent spore numbers, but sufficient inoculum appeared to survive flooding for plants in the following non-rice season to be well colonized (19–33 %) regardless of system. These non-flooded crops appear to replenish depleted AMF propagules.