<p>The Mexican Duck (<i>Anas diazi</i>) is a quasi-endemic North American dabbling duck whose evolutionary history is marked by recent Pleistocene divergence and ongoing introgressive hybridization with the Mallard (<i>Anas platyrhynchos</i>). Because the two species are morphologically and genomically very similar, identifying where their genomes differ structurally is central to understanding how species integrity is maintained under gene flow. Here we present the first highly contiguous de novo genome assembly of <i>A. diazi</i> (PacBio HiFi) and use it to map chromosomal inversions across the phylogeny of the mallard complex. k-mer profiling revealed high heterozygosity (1.08%), and read-depth haplotype purging recovered an accurate 1.19 Gb haploid consensus (BUSCO 95.7%). Using independent, orientation-aware approaches—including read-based structural-variant detection and phylogenetic polarization—we find that structural differences between <i>A. diazi</i> and the Mallard are numerous but small (kb-scale), and strongly enriched on the Z chromosome. Loci within these species-specific inversions (e.g., PIK3C3, RIT2, and DIPK2B) exhibit high structural protein conservation, while functional annotation highlights post-transcriptional mechanisms. Furthermore, the capture of master non-coding RNAs within these rearrangements, including the spliceosomal U1 and the nucleolar SNORA5, provides a mechanism for species-specific alternative splicing and translational control. Ultimately, we find no evidence for macro-inversion ‘supergenes’; instead, the Mexican Duck maintains its divergence through fine-scale, Z-concentrated and post-transcriptional rewiring, consistent with the genomic architecture of recently diverged, hybridizing lineages.</p>