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ObjectivePulicaria gnaphalodes (Vent.) Boiss, known as Kak-Kosh, is a desert-adapted species that has been widely distributed throughout Iran. This plant is a source of flavonoids and terpenes that are used in traditional medicine. Considering the medicinal importance of this plant, the aim of this research was to investigate the effectiveness of molecular and morphological markers to separate the populations.Materials and methodsIn this research, 20 populations of this species were collected from Kerman, Fars, Yazd and Hormozgan provinces and their genetic diversity was analyzed using 10 morphological traits and 25 ISSR primers. Sampling for genetic and morphological studies were carried out in spring and late summer, respectively.ResultsA total of 150 ISSR marker fragments were scored and 139 bands were found to be polymorphic [the percentage of polymorphic bands (PPB): 92.67%]. The average number of effective alleles (Ne) and expected Heterozygosity (uHe) for the amplification products were 1.470 and 0.288 respectively. Both Principal Coordinates Analysis (PCoA) and UPGMA cluster analysis supported the clustering of all the populations into two groups. Small cluster contained populations 15, 18 and 19 and other populations were placed in a large Cluster. A weak relationship was observed between genetic diversity and GIS data. The Factor Analysis (FA) results for morphological traits detected three principal components with Eigen value greater than one (reproductive, leaf area, and vegetative components), which explained 69.24% of the total variability. These three components explained 28.77, 21.05 and 19.42 percentage of variability respectively. The FA analysis separated a group from the other populations.ConclusionsIn the present study, high levels of genetic and morphologic diversity were found between P. gnaphalodes populations. So that geographical separations have a weak effect on genetic diversity of populations. It seems that some probable factors such as perianality, self-incompatibility, pollination system, seed dispersal by wind, and gene flow could support achieving the population in a high level of genetic diversity.