Cannabis sativa L. is a multiple-use plant. However, its cultivation is strictly controlled due to its psychoactive nature and usage in producing drugs such as marijuana, and hashish. In this study, psychoactive type Cannabis samples, which were seized from 29 different locations of Turkey, were used. Interests were to identify the genetic relatedness of the seized samples and to partition molecular variance between and within populations. Randomly Amplified Polymorphic DNAs were employed for analysis based on single plant material and bulked samples of them. Data were analysed via cluster and principal coordinate analyses (PCoA). Analysis of molecular variance (AMOVA) was performed to obtain variations between and within populations. Cannabis accessions were basically separated into two main groups by PCoA and cluster analyses according to geographical regions. One of them was made up of Cannabis plants, which were seized from mostly western part of Turkey (group 1). The other one was made up of Cannabis plants that were seized from mostly eastern part of Turkey (group 2). It is found that 20.23% of the genetic variation is due to differences between accessions groups while 79.77% of the genetic variation is due to between accessions within accessions groups. Compared to group 1, group 2 showed more variation.