Agrobiodiversity results from the domestication and continued selection of crop and livestock species. Understanding the evolution and population dynamics of agrobiodiversity in terms of its genetic, reproductive, ecological, or anthropogenic dimensions, requires both long-term and contemporary perspectives. Population genetics can supply valuable information about the short- and long-term dynamics of agrobiodiversity by describing the trajectory of the frequency of an allele (a genetic variant) within and among given populations. The resultant information makes it possible to understand the relationship between populations and individuals within populations. It is also particularly pertinent to an understanding of how agrobiodiversity has evolved on different timescales. Advances in modeling population genetics enable hypotheses to be tested on the different drivers that shape crop and animal diversity. With the increasing availability of genomic markers, population genetics offers new opportunities to assess, test, and understand agrobiodiversity dynamics.