Datasets presented here were employed in the main work “Spatial structure and soil properties shape local community structure of plant-parasitic nematodes in cultivated olive trees in southern Spain” Archidona-Yuste et al., 2020. In this research, we aimed to unravel the diversity of plant-parasitic nematodes (PPN) associated with cultivated olive (Olea europaea subsp. europaea var. europaea) in southern Spain, Andalusia. The olive growing area of Andalusia is of high agriculture and socio-economic importance with an extensive distribution of this crop. To this end, we conducted a systematic survey comprising 376 commercial olive orchards covering the diversity of cropping systems applied. Data showed 128 species of PPN belonging to 38 genera and to 13 families. In addition, an extensive data set regarding to potential factors in structuring the community patterns of PPN found in the 376 commercial olive orchards sampled is provided. Three variables data set were compiled including above-ground environment, soil and agronomic management. Overall, 48 explanatory variables were selected as determinist processes on shaping the diversity of PPN. Finally, data also showed the values regarding to the partition of beta diversity into contributions of single sites to overall beta diversity (LCBD) and intro contributions of individual species to overall beta diversity (SCBD). Data may serve as benchmarks for other groups working in the field of PPN diversity associated with crops and of belowground communities and ecosystems., This research is part of the PhD project of the first author and was supported by grant AGL2012-37521 from Ministerio de Economía y Competitividad of Spain, grant 219262 ArimNET-ERANET FP7 2012–2015 Project PESTOLIVE and grant P12AGR 1486 Consejería de Economía, Innvovación y Ciencia of the Junta de Andalucía, and Union Europea, Fondo Europeo de Desarrollo regional, ‘Una manera de hacer Europa’. A. Archidona-Yuste was a recipient of research contract BES-2013063495 from Ministerio de Economía y Competitividad, Spain; and at present is a recipient of Humboldt Research Fellowship for Postdoctoral Researchers at Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany., Peer reviewed