Species delimitation in morphologically plastic plant lineages remains a persistent challenge, often leading to taxonomic instability and inflated species numbers. The genus Smilax exemplifies such complexity, particularly within the S. ovalifolia–S. wightii–S. zeylanica complex, which has long been subject to taxonomic uncertainties. Within this complex, S. ovalifolia represents a key reference lineage, exhibiting comparatively stable morphological and anatomical traits that contrast with the pronounced variability observed in S. wightii and S. zeylanica. Building on this contrast, we integrate restriction-site associated DNA sequencing (RAD-seq) with detailed morphological, anatomical, and phylogenetic analyses to reassess species limits and lineage relationships. Genome-wide data provide a framework for evaluating evolutionary cohesion and reveal patterns of divergence not evident from morphology alone. Evidence from molecular phylogenetic analyses, neighbour-joining networks, and population genetic structure consistently supports the genetic distinctiveness of S. ovalifolia, while demonstrating a lack of meaningful genetic separation between S. wightii and S. zeylanica. Instead, these two taxa form a single evolutionary lineage rather than independently evolving species. Levels of genetic differentiation among sampled individuals are low and appear to be influenced by geographic distance and ongoing gene flow, highlighting how population structure and phenotypic plasticity influence morphological variation, potentially leading to misinterpretation in taxonomic assessments. This reassessment clarifies species boundaries in a taxonomically problematic group and highlights the need for multi-evidence approaches when evaluating species limits in morphologically plastic taxa.
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