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.