Agroecology is based on the optimization of ecological processes occurring in agrosystems, especially by improving beneficial interactions among organisms. Recent studies have provided evidence that the ability of plants to interact with free-living soil organisms can be influenced by plant breeding. The upland rice breeding programme in the Highlands of Madagascar aims to develop cultivars that are adapted to local climatic, soil fertility and pest constraints. However, it is still unknown whether this genetic improvement alters rice cultivar abilities to interact with free-living soil plant-mutualistic organisms such as earthworms. We assessed in mesocosms the response of six upland rice cultivars commonly used by farmers in the Highlands of Madagascar to the presence of the endogeic earthworm Pontoscolex corethrurus. Plant nutrition and growth-related traits were measured after eight weeks of growth. These traits were significantly improved in the presence of P. corethrurus for all cultivars compared to the control treatment. However, the magnitudes of earthworm effects on plant traits were strongly variable and were dependent on specific rice cultivars. Agronomic and phylogenetic distance matrices were computed using agronomic data and available phylogenetic data of the rice cultivars. We did not detect significant correlations between cultivar responses to earthworm inoculation and agronomic or phylogenetic distances. Our results suggest that (i) the ability of rice to exploit beneficial interactions involving freeliving soil organisms is influenced by its genetic background, but (ii) the loss of earthworm-interactive abilities of rice crops is independent of the genetic distance among cultivars and breeders? agronomic criteria. Our findings are significant for attempts to use rice cultivars that optimize plant-soil interactions within agroecological practices and highlight the need to integrate free-living soil partners as life-long plant partners in future strategies for plant breeding.