Phylogeography is the study of geographic distributions of genetic lineages and processes that shape them.

Sequencing of plastids regions, like chloroplasts and mitochondria, have been extensively used in phylogeographical analyses. Plastids have haploid genomes and do not recombine, making their historical lineage easier to follow.

A plastid only represents a single locus and does therefore not reflect the true branching of speciation events in history. Thus, analyses of several loci, including both plastid and nuclear genes, are beneficial when mapping a species phylogeography.