In Cameroon, oil palm ( Elaeis guineensis Jacq.) is of economic importance. However, it is affected by vascular wilt presumed to be caused by Fusarium oxysporum f. sp. elaeidis (FOE). Accurate species identification requires molecular-based comparisons. The aim of this work was to molecularly identify Fusarium species associated with diseased oil palms and to determine the pathogenicity of selected isolates. Fungal samples of diseased palms were collected from the canopies and the soil of five oil palm estates of the Cameroon Development Corporation and characterized by sequencing and comparing the translation elongation factor 1a gene. The results revealed the presence of FOE from approximately 80% of the isolates. Cameroonian isolate within FOE clade 1 exhibited the greatest variability grouping with isolates from Suriname, Brazil and Democratic Republic of Congo. Other isolates found in FOE clade 2 formed a unique group which was comprised solely of isolates originating from Cameroon. Twenty-two isolates were chosen for pathogenicity tests. After a short time, 14 isolates were found to be pathogenic to oil palm seedlings. This study revealed the pathogenicity of FOE isolates from Cameroon and demonstrated that FOE in Africa is more diverse than previously reported, including a lineage not previously observed outside of Cameroon. Comparisons between all isolates will ultimately aid to devise appropriate control mechanisms and better pathogen detection methods.