Sunflower is an important edible oilseed crop in India. The major constraint in profitable sunflower cultivation is the susceptibility to Alternaria leaf spot / blight caused by A. helianthi. This has necessitated to study the implications of seed borne nature of A. helianthi of sunflower on seed quality and to find out suitable method for detection of A. helianthi. Studies on cultural, morphological and molecular variation of A. helianthi isolates collected from different locations in Andhra Pradesh were also made. Significant adverse effects of A. helianthi on seed quality parameters viz., germination, seed vigour and moisture content and oil content were also observed. Among different detection methods, Sunflower leaf extract medium (SLEM) was found best in detection of the pathogen in the infected seed samples. Molecular variability of A. helianthi isolates using RAPD analysis with 43 random primers indicated distinct RAPD bands in OPM 16, OPC11 and OPBC 2 markers. Irrespective of districts and genotypes, isolates collected from sunflower seed samples does not exhibit any correlation between cultural, morphological and molecular characters studied.