Plant-parasitic nematodes have traditionally been studied in agricultural systems, where they can be pests of importance on a wide range of crops. Nevertheless, nematode ecology in natural ecosystems is receiving increasing interest because of the role of nematodes in soil food webs, nutrient cycling, influences on vegetation composition, and because of their indicator value. In natural ecosystems, plant-parasitic nematode populations can be controlled by bottom-up, horizontal and top-down mechanisms, with more than one mechanism acting upon a given population. Moreover, in natural ecosystems soil nematodes inhabit probably more heterogeneous environment than in agricultural soils. New breakthroughs are to be expected when new molecular-based methods can be used for nematode research in natural ecosystems. Thus far, nematode ecology has strongly relied on coupling conventional abundance and diversity measurements with conceptual population ecology. Biochemical and molecular methods are changing our understanding of naturally co-evolved multitrophic plant-nematode-antagonist interactions in nature, the inter-connections within the soil food web and the extent to which nematodes are involved in many, disparate, soil processes. We foresee that finer nematode interactions that lead to their management and control can only be fully understood through the joint effort of different research disciplines that investigate such interactions from the molecular to the ecosystem level.