Vascular wilt disease caused by Fusarium oxysporum f. sp. elaeidis (Foe) has devasted oil palm in west and central Africa. This study investigates the spatial distribution of Foe, whereby non-random, clustered patterns of the disease were recorded in four separate plantations in Ghana; infection from tree to tree via elongating roots therefore plays a more significant role than aerial distribution by conidiospores, with management implications. Control of Foe with disease-resistant palm lines can depend on the genetic variability of Foe isolates. Twenty-two putative Foe isolates from several African countries, including Ghana, were obtained from oil palms in infected areas for phylogenetic analysis along with 19 fungal outgroups, using the TEF-1α gene. The data showed Foe isolates have a monophyletic origin, and therefore limited diversity. Palm adapted isolates of F. oxysporum appear to have evolved independently, as ff. spp. elaeidis, albedinis and canariensis were nested into three independent groups. Slowly developing (chronic) and fast, severe (acute) Fusarium wilt are both evident in plantations and we provide preliminary evidence that Foe isolates’ different aggressiveness might contribute to this variation. Sampling for Foe infection from xylem in extracted stem cores revealed the deficiency of field surveys based only on visual symptoms.