Integrative taxonomy offers a powerful approach to clarify species boundaries and enhance the utility of wild germplasm in breeding programs. The genus Citrus and its wild relatives harbor rich genetic diversity with the potential to enhance crop resilience under climatic stress. Yet, frequent hybridization, polyploidy, and overlapping morphological traits have created taxonomic ambiguities that constrain their systematic use. This study integrates molecular and morphological evidence to resolve classification challenges and identify lineages associated with stress tolerance traits. Morphological characterization employed key descriptors such as leaf morphology, fruit architecture, and reproductive traits, while molecular analyses utilized chloroplast and nuclear DNA markers together with genome-wide SNP data. Phylogenetic reconstructions provided improved resolution of taxonomic relationships, revealing distinct clades that correspond with adaptations to salinity, drought, and temperature extremes. Comparative analyses further highlighted taxonomic groups enriched for allelic variants associated with stress-responsive pathways. By resolving taxonomic uncertainties, this integrative framework strengthens the use of wild Citrus germplasm in breeding climate-resilient varieties, advancing sustainable fruit production and food security.