The study focused on the morphological and chemical characteristics of 200 Hymenocrater longiflorus Benth. genotypes found in natural habitats of eight regions in west of Iran. The primary objective of the study was to assess the morphological and phytochemical variability within populations grown in their natural habitats, with the aim of identifying their potential for domestication and utilization in pre-breeding programs. The plant height (PH) ranged from 50.32 to 69.65 cm, with the highest observed in population P8. The internode distances ranged from 4.7 to 6.47 cm, with the maximum distance found in P4. Flower lengths varied from 1.95 to 2.45 cm, with the minimum and maximum values observed in P4 and P3, respectively. The highest leaf length (5.20 cm) and width (3.87 cm) were recorded in P2. The aerial parts of the plant were utilized to extraction and determine the essential oil (EO) content and composition, which ranged from 0.40 to 0.78% (v/w). The analysis of EO by gas chromatography (GC) and gas chromatography mass spectrometry (GC/MS) identified 26 compounds, constituting 99–99.5% of the EOs. The main compounds in the EO and their percentage range (v/w DW) were tau-cadinol (0.62–55.56), mono (2-ethylhexyl) phthalate (8.10–94.70), elemol (0.21–19.11), β-spathulenol (0.08–14.39), 4-terpineol (0.23–10.19), and β-eudesmol (0.21–9.94). The main chemical groups found in EOs included oxygenated sesquiterpenes (1.12–68.43), and phthalates (9.73–94.72). Cluster analysis revealed three distinct chemotypes: chemotype I (populations 1 and 2) with major components of mono (2-ethylhexyl) phthalate, tau-cadinol, and α-elemol; chemotype II (population 5) rich in mono (2-ethylhexyl) phthalate; and chemotype III (populations 3, 4, 6–8) containing tau-cadinol, β-eudesmol, and 4-terpineol. The study also evaluated total phenolic, total flavonoid, and DPPH free radical scavenging activity in the fifty percent inhibitory concentration (IC50) in leaf and flower samples of the genotypes, along with estimating total anthocyanin content in the flower samples. The total phenolic content (TPC) in leaf and flower samples ranged from 7.89 to 107.18 mg GAE/g DW and 39.98 to 86.62 mg gallic acid equivalent (GAE)/g DW, respectively. Total flavonoid content (TFC) ranged from 81.04 to 143.46 mg QUE/g DW in leaf samples and from 94.82 to 133.26 mg quercetin equivalent (QUE)/g DW in flower samples. DPPHsc IC50 (µg/mL) ranged from 0.65 to 78.74 in leaf samples and from 4.38 to 7.71 in flower samples. Anthocyanin content ranged from 1.89 to 3.75 mg cyanidin-3-glucoside equivalent (C3GE)/g DW among populations. Canonical correspondence analysis and simple correlation demonstrated a strong association and correlations among the studied attributes. The negative correlations between leaf DPPH (DPPH L) IC50 and TFC (− 0.73), TPC (− 0.63), Elemol (− 0.90), and EO (− 0.85) indicate that these compounds have a significant impact on the antioxidant activity of the leaves. Furthermore, Fruit DPPH (DPPH F) IC50 showed a negative correlation with TPC (− 0.79) and TFC (− 0.78), but a positive correlation with flower anthocyanins (0.51), (Z)-β-Farnesene (0.66), and 4-Terpineol (0.57). Circular cluster analysis categorized the genotypes of all individuals in the eight studied populations into three main categories based on all the studied traits, indicating significant variation in phytochemical and morphological traits among populations, surpassing the within-populations variation.