Abstract: A study on cultural, morphological and biochemical variability among the isolates of Phomopsis azadirachtae Sateesh, Bhat and Devaki collected from sixteen districts of Karnataka state, South India was carried out. The isolates were compared for the cultural and biochemical variability. It was observed that the isolates varied considerably for the cultural characteristics such as mycelial growth pattern, colour of the colony, sporulation behaviour, texture of pycnidia, production of alpha and beta conidia and the dimension of conidia produced. Estimation of water soluble mycelial proteins and toxicity of culture filtrate of P. azadirachtae isolates revealed a remarkable difference in the mycelial protein content of the isolates and different isolates exhibited various extent of toxicity on the germination of neem seeds.