Whitefly-transmitted geminiviruses (subgroup III, Geminiviridae) are emerging viral pathogens of cotton, worldwide. Virtually nothing is known about the genetic variability, biological characteristics, or the molecular epidemiology of these new virus pathogens of cotton. The genetically variable core region (550bp) of the coat protein gene was examined as a potentially informative molecular marker by which to identify and track the global distribution of WFT geminiviruses of cotton. This is an essential step toward assessing the risks that these emerging viruses pose to cotton production efforts. Preliminary analyses of geminivirus isolates from North America, Central America and the Caribbean Basin, and Sudan indicate that the core region of the coat protein gene permitted predictions about relationships between virus isolates from cotton, based on subgeographical and major geographical origins, and has potential for distinguishing between virus strains and quasi-species. From these experiments, a database of coat protein gene sequences has been established to permit identification of additional isolates from cotton, and to facilitate the tracking of WFT geminiviruses for molecular epidemiological and subsequent risk assessment objectives. Using this latter information, it will become possible to identify the most important geminiviruses against which disease resistance efforts should be targeted. Further, the availability of a broad suite of cotton geminivirus isolates from both Eastern and Western Hemispheres will permit testing of germplasm and/or genetically engineered cultivars for virus-specificand/or broad spectrum resistance for the first time.