Blight symptoms on pigeonpea were observed in alarming proportion since 2009 onwards in Andhra Pradesh state of India. Alternaria blight infected pigeonpea plants were collected from Andhra Pradesh state of India to isolate and characterize the pathogen. The isolate proved pathogenic on pigeonpea cultivar ICPL 87119. Genetic characteristics were analyzed based on the sequence of the rDNA-internal transcribed spacer (ITS) region. The phylogenetic tree based on rDNA-ITS analysis showed that the Alternaria alternata causing Alternaria blight in pigeonpea is very distinct from the other Alternaria isolate reported from different host. This is the first report of molecular identification of Alternaria alternata causing Alternaria blight in pigeonpea.