Oil palm, Elaeis guineensis Jacq., is an important economic crop in Cameroon. Fusarium is responsible for the most serious oil palm diseases in Cameroon, including a vascular wilt presumed to be caused by Fusarium oxysporum f. sp. elaeidis. Contemporary species identification relies strongly on molecular identification, yet resources for this identification are rare in developing countries. Traditional taxonomy of Fusarium is based on morphological criteria. However, the limited number of morphological characters available has resulted in cryptic Fusarium taxa. The aim of the study was to molecularly identify Fusarium species obtained from diseased palms and compare the isolates in order to devise appropriate control mechanisms and better pathogen detection methods. Samples of diseased palms were collected from the canopies and soil in five oil palm estates of the Cameroon Development Cooperation. Isolates were cultured, single spored and a portion of the translation elongation factor 1a gene was amplified from genomic DNA. The result revealed the presence of Fusarium oxysporum f. sp. elaeidis (FOE) from approximately 80% of the isolations. Cameroonian isolate within FOE clade 1 exhibited the greatest variability. Some grouped with FOE from Suriname and Brazil while others with previously characterized African isolates from Zaire and other isolates form a unique Clade 2 comprising solely of isolates originating from Cameroon. This study reveals that FOE in Africa is more diverse than previously reported and contains lineages not previously observed outside of Cameroon.