Abstract: In present study, morphological traits and RAPD markers were used to analyze variation among different populations of M. chamomilla growing in four different provinces in Southwest of Iran along with some standard cultivars. Variance analysis of morphological traits showed that all evaluated traits were significantly different among populations. Maximum coefficients of variability were belonging to weight of plants (87.94%) and number of flower per plant (62.64%). Dendrogram was drawn based on Euclidean distances from morphological data matrix. All populations were represented into two main groups. With regards to yield of flowers, oil yield, plant height, etc., some populations showed performance equal to standard cultivars. In RAPD analysis 18 selected primers produced 220 bands, of which 205 were polymorphic. The ranges of similarity between populations were varied from 0.15 to 0.78. According to the UPGMA derived dendrogram, at a similarity level of 0.25, the populations were divided into two main groups. With regard to Nei's genetic diversity parameters calculated for different provinces of origins, maximum and minimum number of effective alleles was observed in Khuzestan (1.657) and Fars (1.142) provinces, respectively. The percentage of polymorphic loci (P loci% ), Nei's gene diversity (h) and Shannon's information index (I), calculated for different provinces, indicated that diversity was highest within Khuzestan province (P loci = 90.29%, h = 0.364 and I = 0.528) and lowest within Fars province (P loci = 20.87% , h = 0.16 and I = 0.23). Wide domain of genetic variability revealed in this study could be considered as a gene pool available for German chamomile improvement through selection and hybridization breeding programs. High heterosis effects will be expected for hybrids of these genetically diverse and talent populations.