Abstract: Background and Objective: The fungus of Alternaria solani causing early blight disease on tomato plants and become very important pathogen. Fungi usually have a variation between their populations and this variation affects disease control methods. In Jordan, scarcity of studies on Alternaria solani have been investigated. Hence, this study was designed to characterize the fungus of Alternaria solani isolated from diseased tomato plants grown in Jordan Valley based on molecular methods using sequences of Internal Transcribed Spacer (ITS) region of rDNA. Materials and Methods: Twelve isolates were used and divided into four groups, isolated from diseased tomato plants grown in Jordan valley. Sequences of 12 isolates obtained in this study matched Alternaria solani (LT714700) from GenBank. The unweighted Pair Group Method with Arithmetic Mean (UPGMA) dendrogram showed that there were four groups at similarity coefficient 0.1. Each group contains 3 isolates obtained from diseased tomato plants collected from different farms in the Jordan Valley in early 2012. Results: This study demonstrated that there were variation in the population of Alternaria solani isolated from Tomato plant in Jordan Valley based on the sequences of the ITS region of rDNA. The sequences of the ITS region of rDNA for the 12 Alternaria solani isolates were found to be identical to Alternaria solani (LT714700) in the GenBank. Conclusion: This study showed variations in the population of Alternaria solani. This research is the first to describe Alternaria solani in Jordan based on molecular methods. Moreover, the results of this study will help researcher and farmers in finding the best control methods to Alternaria solani.