This study explores the impact of geographic barriers on the distribution and survival of Mediterranean endemic species, focusing on Centranthus sect. Nervosae, a tetraploid species complex found in Corsica and Sardinia. The aim is to analyse how these barriers influence genetic diversity, population structure, and phylogeographic pattern, thereby impacting conservation strategies and future resilience of the selected study species. Genotyping involved biparental markers (16 nuclear microsatellites for the population genetic survey) and Sanger sequencing of uniparental markers (six plastid sequences for the phylogeographic survey). Screening of microsatellites revealed a diploidisation process, and haplotype fixation in plastid sequence was observed across all populations. Results from both survey methods clearly indicate that isolation and barriers have significantly impacted the genetic structure of populations, subjecting them to genetic drift, bottlenecks and related evolutionary phenomena. Over time, these factors have resulted in the observed low haplotypic variability and nuclear microsatellite diversity. Reduced genetic variability, combined with factors such as inbreeding and genetic drift, highlight the vulnerability of these populations to extinction. Consequently, this multi-approach survey has contributed to defining conservation strategies, stressing the need to preserve genetic diversity and mitigate the impacts of human activities and environmental changes on endemic plant communities in island-like environments. The study emphasises the importance of integrating multiple marker types to deepen our understanding of conservation genetics and evolutionary history, thereby contributing to the assessment, and planning of potential safeguarding strategies for such endemic species.