Cacao genebanks preserve the diversity needed to breed trees for changing climates, emerging diseases, and more resilient production. However, historical mislabeling, synonymy--one genotype recorded under several names--and homonymy--different genotypes sharing one name--can undermine breeding and field recommendations. High-density genotyping can resolve these problems, but routine use may demand more money, laboratory capacity, and data handling than many programs can support. Existing low-density panels are cheaper, yet their markers are often selected without a unified method for comparing identification power, population structure, and trait relevance. Because of these challenges, deeper research is needed to develop compact genotyping systems that preserve the information most useful for germplasm management and breeding.