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Rice production in Southeast Asia is significantly affected by root-parasitic nematodes (RPN). The Green Revolution has encouraged new agricultural practices (e.g. intensive monoculture, high yielding rice variety) to respond to the high rice demand; however, these methods have promoted the spread of these pests. The recent banning of chemical nematicides resulted in a need for alternative sustainable control strategies. In the present study, we assessed the effects of a direct-seeding mulch-based cropping system (DMC) vs conventional plough-based tillages (CT) on soil properties, rice yield and RPN communities during a two-year trial in Cambodia. Our results show that on average the population densities of RPN were significantly higher in DMC than in CT. Molecular identification revealed only two RPN species associated with roots: Meloidogyne graminicola, not previously reported from Cambodia, was predominant and was present throughout the plant's development, whereas Hirschmanniella mucronata was only found at the tillering and milky stages. We conclude that DMC had a significant positive impact on rice yield, despite higher RPN short-term pressure. In order to increase the efficiency of such cropping systems, further studies and an evaluation of the long-term relationships between DMC, the nature of cover crops used, the soil biota including RPN, and rice yield should be conducted.