The present study aimed to test pharmacognosy and molecular study of some Allium species (Amaryllidaceae) using internal transcribed spacer (ITS) gene region collected from Saral area of Kurdistan province, Iran. Three Allium species including Allium tripedale, Allium hooshidaryae and Allium stipitatum was selected to be included in the study. Methanolic extracts of selected species was prepared after drying in ppropriate light and temperature conditions. Ferric reducing assay was used to measure antioxidant capacity of extracts. Total phenolic and total flavonoid contents were measured using the Folin Ciocalteau and aluminum chloride color complex methods, respectively. Furthermore, different pharmacogenosy test was performed to predict of present chemical compounds in studied Alliums. Antimicrobial testing of plant extracts for gram-positive and gram-negative strains was performed by disk diffusion method. The results showed a low to moderate antioxidant capacity of studied Alliums compared to ascorbic acid. Among three studied Alliums, the highest antioxidant capacity belonged to Allium hooshidaryae; however, no significant difference was found between three studied Alliums (p>0.05). Pharmacognosy tests indicated that all studied Alliums contained phenolic, flavonoid and glycosides compounds and Allium stipitatum had the highest number of chemical compounds. Antimicrobial tests indicated that Allium stipitatum had greatest inhibitory effects on the bacterial, while Allium hooshidaryae was approximately ineffective. Among the studied bacteria, Pseudomonas aeruginosa strain was approximately resistance against studied Alliums antimicrobial activity. Moreover, Allium stipitatum showed the highest ability to inhibit bacteria growth against Staphylococcus aureus in all concentrations. The results of fragment sequencing revealed that used primers amplified a 900 bps fragment of which 383 nucleotides were vary between used species. The phylogeny analysis showed monophyletic clade for studied species among Melanocrommyum subgenus and close relationship between species. However, they were separated in three different sections.
