Abstract Understanding the genomic basis of diversification is a central goal in evolutionary biology. In recent years, the development and use of pangenomes, a genomic representation of multiple individuals within a lineage (a set of related populations, subspecies, ecotypes, or species), has enabled researchers to differentiate between DNA sequences shared by all individuals of a given lineage (core regions) from those present only in some individuals (accessory or variable regions). Differentiating between core and accessory regions has highlighted a key limitation of relying on a single reference genome: It captures the genetic code of only one individual and this biases genomic analyses and our understanding of diversification. Here, we propose that by identifying genes associated with both core and accessory regions, we can deepen our understanding of the processes underlying diversification. We suggest that analyzing pangenomes and accessory regions will provide deeper insights into diversification, hybridization, and the genetic basis of adaptation and speciation.