Background <p>Extreme environments provide powerful natural laboratories for studying evolutionary convergence across taxa. While convergent phenotypes frequently evolve in response to similar selective pressures, consistent molecular signatures at the nucleotide level are often elusive, potentially due to overlooked genetic variants such as structural variants. Here, we leverage recent advances in long-read sequencing and pangenome approaches to investigate the role of structural variants in repeated adaptation to toxic springs rich in hydrogen sulfide (H₂S) across multiple independently evolved populations within the <i>Poecilia mexicana</i> species complex.</p> Results <p>We identified more than 99,000 structural variants over 50 base pairs in length, including insertions, deletions, duplications and inversions, using complementary graph- and read-based methods. We then integrated these with population genomic data and RNA-sequencing data to detect variants in highly differentiated regions between ecotypes and assess their functional impacts. Structural variants in both coding and regulatory regions were enriched in genes involved in sulfide metabolism and ion transport, including <i>ethe1</i>, <i>slc13a1</i>, and <i>sqor</i>. We found ecotype-specific structural variants in promoter and intronic regions of key detoxification genes that exhibited elevated expression in H₂S-adapted populations.</p> Conclusions <p>Our findings suggest that structural variation may contribute to adaptive phenotypes and should be considered in studies of genomic convergence.</p>