Root-knot nematodes of the genus Meloidogyne are recognised worldwide as a major production constraint in crops of primary economic importance. Knowledge of their diversity and prevalence, as well as the major environmental and agronomical cues for understanding their distribution in specific areas is of vital importance for designing control measures to reduce significant damage. We provide the first detailed information on the diversity, distribution and levels of Meloidogyne species infecting wild and cultivated olive soils in a wide-region in southern Spain that included 499 sampling sites. Overall Meloidogyne spp. were found in 6.6% of sampled olive plants, with 6.6% and 6.5% for cultivated and wild olive, respectively. We identified five previously described Meloidogyne spp. (Meloidogyne arenaria, M. baetica, M. hapla, M. incognita, M. javanica) and one new species (Meloidogyne oleae sp. nov.) which, characterized using integrative taxonomy, increases the known biodiversity of Meloidogyne spp. affecting olive. Meloidogyne arenaria and M. incognita were only found infecting cultivated olive varieties, while, M. baetica was only found infecting wild olive. Three major parameters drive the distribution of Meloidogyne spp. in cultivated olives in southern Spain, cover vegetation on alley, irrigation and soil texture, but different species respond differently to them. In particular the presence of M. incognita is highly correlated with sandy loamy soils, the presence of M. javanica with irrigated soils and cover vegetation, while the presence of M. arenaria is correlated with the absence of cover vegetation on alley and absence of irrigation. These parameters likely influence the selection of each particular Meloidogyne species from a major dispersal source, such as the rooted plantlets used to establish the orchards.