Gene flow between morphologically differentiated populations of Thomomys bottae has led to detectable shifts in population morphology over a relatively short period of time (20 to 60 years). Temporal samples from museum collections make it possible to document directed changes in the subspecies chrysonotus from the Ehrenberg area of Arizona in comparison with seemingly random temporal variation in other populations along the Colorado River. The most likely scenario involves pocket gophers from the California side of the river becoming established on the Arizona side south of Ehrenberg and serving as a source of gene flow into the Ehrenberg area. Electromorphic data support such a scenario. The views of mammalogists have changed over time with regard to the relationships among these pocket gopher populations. This has most likely been due to the dynamic nature of these populations whereby their genetic relationships have indeed shifted over a relatively short period of time. Differences in analytical approaches have also led, in part, to different interpretations.