Background <p><i>Chouardia litardierei</i>, commonly known as amethyst meadow squill, is a plant species characterized by profound ecological plasti vcity. As a wild, non-model species, it represents a suitable system for gaining insights into the genomic background of the local adaptation process. By implementing a genome-environment and genome-wide association studies, we sought to investigate the genomic regions related to the local adaptation and the development of several reproduction-related traits in <i>C. litardierei</i>: for sexual reproduction, Average Height of Inflorescences (AHI) and Total Flower Count (TFC) per genotype, and for asexual reproduction, Bulb Count (BC) per genotype.</p> Results <p>A genome-environment association (GEA) study of selected <i>C. litardierei</i> populations revealed the precipitation of the coldest quarter as the bioclimatic variable with the most substantial influence on detected variability, with numerous candidate genes detected and functionally characterized. To evaluate the genetic basis of selected reproduction-related traits we combined phenotypic data of 214 individuals raised as a part of a common garden experiment with ddRADseq genotyping results. After implementing various single- and multi-locus GWAS models for all traits, multiple candidate loci affecting their development were recognized. In addition, high, narrow-sense heritability estimates indicated that genetic factors accounted for over 55% of the phenotypic variance in each trait. Notably, the highest heritability estimate was observed for the Average Height of Inflorescences (71.95%), suggesting its crucial role in reproductive success. Functional annotation of the associated genomic regions identified key protein families involved in reproduction-related biological pathways, including nitrogen metabolism, phytohormone regulation, and floral organs development.</p> Conclusion <p>By implementing GEA and GWAS, we revealed a list of candidate loci significantly associated with adaptation to specific environmental variables and morphological traits related to sexual and asexual reproduction in <i>C. litardierei</i>. These findings provide a foundation for a deeper understanding of the molecular mechanisms driving the local adaptation processes occurring among <i>C. litardierei</i> populations from different habitat types. At the same time, the high heritability estimates of morphological traits further underscore the significance of genetic factors in the local adaptation process.</p>