Early blight disease caused by Alternaria sp. is one of the most devastating diseases of Solanaceous crops widely distributed in Sudan. The aim of this study was to determine the genetic variation among different Alternaria isolates recovered from different Solanaceae crops showing typical symptoms of early blight disease. Infected leaves of tomato, potato, eggplant and pepper were collected from different geographical zones in Sudan. The recovered fungal isolates were identified to the genus level based on cultural and morphological characteristics. Five representative isolates were sent to the CABI Bioscience, U.K. for confirmation. The genetic relationship among the isolates was determined using the amplified fragments length polymorphism (AFLP) technique and the generated data were used to create similarity matrices using the PAST 3.01 software package. Dendrograms were constructed based on Jaccard’s similarity coefficients. A total of 70 fungal isolates was recovered from the tested plants and all of them showed morphological characteristics typical of Alternaria spp. The conidia appeared in multiple-branched chains with spore sizes in the range of 2.38−13.09 μm × 12.30−43.63 μm. Therefore, the isolates were identified as Alternaria alternata (Fr.) Keissl. The identification was then confirmed by CABI.AFLPbased dendrogram which revealed five clusters with a significant cophenetic correlation coefficient (r = 0.834) between the dendrogram and the original similarity matrix irrespective of their geographical origins. Eighteen (75%) of the Alternaria isolated from tomato leaves were clustered together in cluster I and five isolates formed two separate clusters, viz. cluster IV (T-Kh5 and T-H1) and cluster V (T-H4 and T-Med2). The remaining isolate, T-Am5, grouped with one of the potato isolates in cluster III. The other isolates which were recovered from potato, pepper and eggplants were all separated from the tomato isolates in the largest cluster.