An increased need to understand the genetic relationships among cacao (Theobroma cacao) germplasm exists to identify cultivars that possess resistance to witches' broom disease (caused by Crinipellis perniciosa). Loss of production due to witches' broom disease in important cacao-growing areas, such as Bahia, Brazil, has generated a strong demand for disease-resistant varieties. Varieties based on single sources of resistance have been released; however, other genotypes are needed to enlarge the genetic diversity of cultivars in breeding programs. A core collection has been created to represent the range of genetic diversity available among the more than 600 cacao accessions at Centro de Pesquisa do Cacau (CEPEC). The cacao core facilitates access to the collection and is intended to enhance its use. This core collection was created from RAPD marker-based estimates of genetic distance among a subset of 270 accessions from the entire collection. The subset was sampled based on 1) witches' broom disease resistance data, 2) random sampling of the collection, and 3) random sampling of recently acquired accessions. Differences in RAPD marker frequencies were used to identify accessions in a witches' broom disease breeding program that contribute to the genetic diversity of the collection as a whole. In addition, differences in RAPD marker frequency allowed the comparison between accessions in the original collection and those acquired from new geographic regions that may expand the collection's genetic diversity.