Amphioxus are small marine chordates that have broad ecological ranges, yet as adults form local settlements and exhibit limited mobility. Genomic surveys of two amphioxus species have suggested that they rank among the most genetically diverse metazoans. Here, we present the first accurate assessment of genomic diversity in the European amphioxus ( Branchiostoma lanceolatum ) and investigate the processes underlying this diversity. We leverage high-coverage whole-genome sequencing data from multiple individuals sampled at two geographically distant Atlantic and Mediterranean locations. Consistent with previous estimates in other amphioxus species, we measure exceptionally high genomic diversity, with an average heterozygosity of 2.73% in B. lanceolatum . Despite the large geographic separation between sampling sites, population differentiation is minimal, indicating extensive gene flow among distant adult settlements. Phylogenetic analyses combined with population genetic simulations confirm that this elevated genomic diversity is primarily driven by a large effective population size. Although adult amphioxus have limited mobility, our results indicate that long-distance larval dispersal mediated by ocean currents is sufficient to generate a near-panmictic population structure across their broad ecological range. ### Competing Interest Statement The authors have declared no competing interest. Swiss National Science Foundation, 207853 Agence Nationale de la Recherche, ANR-21-CE13-0034

Genomic structural variation is an important component of genetic variation in natural populations. By assembling and analyzing multiple high-quality genomes within a species or clade, pangenomes capture variation that can be missed by reference-based genomics at both the sequence and the genic levels. Although pangenomes are nascent tools for animals compared with other taxa, they have already unveiled novel insights into genome evolution, adaptation, the genomic basis of organismal traits, and conservation genomics. We highlight the rapid progress and unique ecological and evolutionary discoveries emerging from applying pangenome tools to diverse natural populations. We conclude that pangenomes are fundamentally shifting the field by revealing structural variants as a key source of adaptive potential and genomic diversity previously missed by single-reference methods.