Abstract: The random amplified polymorphic DNA (RAPD) markers were used to study the nature of genome differentiation between natural populations of L. sativus. The degree of band sharing was used as a criterion to calculate the genetic distance and to construct phylogenetic trees. The 28 populations from Pakistan, India and Ethiopia differed in the amount of β- N - oxalyl -L- a, β- diamino propionic acid (β-ODAP) in their kernels. Irrespective of their geographical diversity high toxin and low toxin varieties clustered into genetic groups in the phylogenetic tree. The results would suggest that the variation between populations in the neurotoxin content is governed by genetic factors and has occurred for this trait during evolution