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German chamomile (Matricaria chamomilla L.) is an s an annual plant of the composite family Asteraceae. This plant is native to the Mediterranean region, and some researchers have reported its origins in Asia. The aim of this study was to investigate the genetic diversity of nine chamomile populations using the SCoT marker. Ten SCoT primers were used. A total of 141 bands were produced, of which 140 bands (96.5%) showed polymorphism. Cluster analysis was performed using UPGMA algorithm based on Jaccard's coefficient of similarity. The results of cluster analysis and principal components analysis divided the chamomile population into four groups. The results of the analysis of molecular variance (AMOVA) showed that the inter-group variation was greater than the intra-group variation, so that 55% of variation was related to the diversity among the groups. The results of this study showed that SCoT markers have high efficiency in determining the genetic diversity and relationships of the chamomile populations.