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Introduction: Centranthus kellereri is a Bulgarian endemic plant species, found only in two locations in the world: The Balkans Mountains (Stara Planina), above the town of Vratsa, and The Pirin Mountains, above the town of Bansko, Bulgaria. Being endemic and endangered species precluded any significant research on it. The hypothesis of this study was that the populations of C. kellereri may represent genetically, phytochemically, and morphologically distinct forms and these will differentiate from C. ruber. Furthermore, C. kellereri possibly imperfect embryology may preclude its more widespread distribution under natural conditions. Results: This study revealed the phytochemical profile, antioxidant activity, embryology, surface microstructural morphological traits, and genetic differences between the C. kellereri plants from the only two natural populations and compares them to the ones of the related and better-known plant C. ruber. The essential oil (EO) content in aboveground plant parts and in roots was generally low and the EO composition varied significantly as a function of plant part, year of sampling, location, and species. Methylvaleric acid was a major EO constituent in the C. kellereri EO, ranging between 60.2% and 71.7% of the total EO. The EO included monoterpenes, sequiterpenes, long-chain alkanes and fatty acids. Phytochemical analyses of plant tissue revealed the occurrence of 32 compounds that were tentatively identified as 6 simple phenolics, 18 flavonoids, 1 quinone, 1 lipid, 1 alkaloid, 2 diterpenes, and 3 triterpenes. There were differences in detected compounds between the C. kellereri plants at the two locations and between the roots and shoots in both species. The total phenols and flavonoids varied between the two species but were also dissimilar between the plants from the two populations of C. kelleri. Free radical scavenging activity, measured with ABTS and DPPH in aqueous and methanol extracts, had similar values; however, overall, C. kellereri from Vratsa showed the highest antioxidant activity while C. ruber had the lowest activity. Genetic analyses showed a clear differentiation between C. kellereri and C. ruber, and between the two populations of C. kellereri. Embryological studies revealed the peculiarities of the male and female generative spheres of the two species that were defined as being sexually reproducing. The pollen had high viability; however, the low viability of seeds demonstrated possible high sensitivity of C. kellereri to the environmental conditions, perhaps the main factor modifying and restricting the population sizes. The SEM analyses exposed differences in surface microstructural traits between the species (C. kellereri and C. ruber) but also between the two populations of C. kellereri. The observed dissimilarities in genetic makeup, micromorphological characteristics, and phytochemical composition strongly indicate that the two populations can be classified as distinct subspecies or varieties of C. kellereri; var. pirinensis and var. balkanensis. Further research is needed to introduce C. kellereri into culture and develop it as a high-value specialty crop or ornamental in order to conserve C. kellereri natural populations. C. kellereri may be utilized as a source for phytochemicals of interest and as an ornamental plant like C. ruber; however, it may have a greater environmental plasticity and adaptation as evidenced by its current locations. [ABSTRACT FROM AUTHOR]