We applied fifteen microsatellite markers for molecular identification of cocoa (Theobroma cacao L.) varieties and their beans in the production chain, and for distinguishing ‘fine or flavour’ cocoa from bulk varieties. Thirteen markers were from Lanaud et al. (1999) and listed in the International Cocoa Germplasm Database. All of these mTcCIR markers are dinucleotide repeat markers, which means that the amplification of stutter bands alone may make the genotyping less reliable. We added two markers developed on a tri- and a pentanucleotide repeat. The advantage of these is that the alleles are at least three or five nucleotides apart, which facilitates scoring. In our set of varieties tested, the most polymorphic markers were mTcCIR6, mTcCIR12, mTcCIR15, mTcCIR18, mTcCIR33 and mTcCIR37, which had an effective number of alleles of 4 or more. Among representative varieties of the Nacional, Trinitario and Criollo types, most varieties were clearly differentiated, while duplicate samples from different countries had identical patterns, although some mislabelling occurred. Bulk and ‘fine or flavour’ varieties were clearly distinguished, but they did not form two genetically distinct groups. The genotypes of ICS 1 beans from different plantations indicated various numbers of pollinators and proportions of self-pollination. The bean genotypes enabled reconstruction of the genotype of the maternal parent, and they contained information on the number and type of pollen donors of each plantation. If plantations have unique genotypes or combinations of genotypes, it may be possible to distinguish them based on the combined genotypes of a set of beans.