When suitably deployed, genetic markers facilitate all phases of plant genetic resource management, from acquisition through enhancement. This paper will review the kinds of plant genetic resources and genetic markers, analytical methods for marker data, and specific applications of genetic markers to plant genetic resource management, such as (i) assessing a collection's “gaps” and redundancy; sampling strategies; characterizing newly acquired germplasm; maintaining “trueness to type”; monitoring genetic shifts; monitoring germplasm viability and health; developing optimal utilization strategies from genetic marker data; exploiting associations among horticulturally meritorious traits and genetic markers. Finally, general conclusions and forecasts regarding future prospects for applying genetic markers to these tasks will be presented.