• Whole-genome resequencing of 177 Phalaenopsis accessions generated 19.7 million high-quality SNPs. • Two independent inoculation tests quantified YLD resistance by AUDPC with high heritability (H² = 0.85). • DAPC resolved four genetic clusters differing in YLD susceptibility and key ornamental traits. • GWAS integrating single- and multi-locus models identified resistance-associated loci on chromosomes 2, 5, 8, and 16. The orchid industry in Taiwan is dominated by Phalaenopsis spp., which cons