Three species of genus Asparagus native to Lake Van Basin of Turkey were analyzed using internal transcribed spacer (ITS) and cpDNA trnL intron sequence. Furthermore, these species were screened for their antioxidant activity and total phenolic and flavonoid contents. Phylogenetic analysis based on ITS data revealed two clades: the first clade consisted of Asparagus persicus and Asparagus officinalis, and clade II consisted of Asparagus palaestinus. Similarly, phylogenetic analysis using trnL intron sequence revealed two clades. In term of total phenolic content and total flavonoid content, the highest value were measured for acetone extract of Asparagus persicus sample No. 2 and Asparagus persicus sample No. 6, respectively. The highest antioxidant activity using FRAP assay was found for Asparagus persicus sample No. 3. We concluded that these species could be useful for increasing genetic diversity among cultivated species and for breeding.