Cacao (Theobroma cacao L.) is an important tree crop for millions of farmers and for the multi-billion dollar chocolate industry but is derived from a limited genetic diversity. The centre of diversity of cacao is being deforested, thereby increasing genetic erosion, but fortunately a wealth of genetic diversity exists in global cacao collections. This chapter discusses the role and types of gene banks to capture genetic diversity. The chapter deals with the distinction between cacao gene banks and other gene banks and examines how this affects the management and estimation of genetic diversity. The chapter advocates an SNP panel for fingerprinting and addresses molecular marker-assisted management with the objective of comparing global collections and formulating a core collection.