Capparis spinosa is a xerophytic shrub that has amazing capacity for surviving in challenging circumstances. Therapeutic and pharmacological benefits of this plant species, and its culinary applications, are of significant interest. Various bioactive constituents discovered throughout several organs contribute to its phytochemical relevance, and its cultivation has significant potential commercial benefit. Furthermore, the broad heterogeneity of C. spinosa has made taxonomic classification challenging, and paucity of genetic investigations has led to uncertainty among numerous authors. Recent study epitomizes dataset regarding C. spinosa encompasses taxonomical, phytochemical and molecular investigation. Three Egyptian endemic varieties of C. spinosa; canescens, deserti, inermis were genetically identified using two marker approaches including inter simple sequence repeat (ISSR) and start codon targeted polymorphism (SCoT). Five primers for each approach totaled ten in total for the analysis. ISSR and SCoT primers generated 28 and 40 bands overall, respectively. Polymorphism levels ranged between 64.28 to 67.50% with ISSR and SCoT examination, respectively. Furthermore, chemo-taxonomic clustering employing UV-spectroscopic analysis besides phenolic content was coupled with unsupervised chemometric tools of Principal Components Analysis (PCA) and Hierarchical Cluster Analysis (HCA). Through molecular and phytochemical investigations, interspecific relationships among canescens and deserti varieties have been verified. Additionally, inermis variety was identified as a monotypic variety. Flavonoid content coincided with the conclusion, which was proved through different expression of phenylpropanoid biosynthetic genes. This research suggests raising var. inermis to the species level, namely Capparis orientalis, demonstrating that chemotaxonomic information can mirror evolutionary connections between caper varieties and sheds light on the need of combining molecular and chemo-taxonomy's advantages to clarify the evolutionary connections within this species.