Background <p>Natural selection plays a pivotal role in maintaining genetic boundaries by counteracting the potentially deleterious effects of alleles introduced through hybridization. Here, we investigated this process through a comparative population genomic analysis of three endemic varieties of <i>Picea likiangensis</i> (vars. <i>likiangensis</i>, <i>linzhiensis</i>, and <i>rubescens</i>) across the Qinghai-Tibetan Plateau (QTP) and adjacent regions.</p> Results <p>Leveraging genome-wide single nucleotide polymorphism (SNP) data from 193 individuals, we documented pervasive genetic admixture among these taxa, yet observed a pronounced asymmetric pattern of introgression: synonymous polymorphisms (<i>H</i>s) exhibited significantly higher introgression levels than non-synonymous polymorphisms (<i>H</i>n). This pattern indicates that purifying selection may actively eliminate maladaptive non-synonymous mutations, whereas neutrally evolving loci continue to undergo gene flow. Moreover, the relative hybrid index (ω_<i>H</i> = <i>H</i>n/<i>H</i>s) was lower in populations adjacent to pure <i>rubescens</i> stands, suggesting stronger selection against introgressed alleles in the core range of the recipient taxon rather than a simple effect of geographic distance. In addition, recombination rate was significantly associated with introgression bias, implying that recombination facilitates the removal of maladaptive genomic segments following hybridization.</p> Conclusions <p>Our findings underscore the pivotal role of comparative population genomics in elucidating how natural selection shapes introgression and contributes to the maintenance of genetic boundaries during speciation.</p>