The clonal propagation of T. cacao by somatic embryogenesis (SE) is a promising approach to multiply elite genotypes. Assessing clonal fidelity in plants regenerated from somatic embryos is the first step toward ensuring genetic uniformity in the mass production of planting material. This study assessed the genetic stability of cacao plantlets propagated by SE and conventional grafting for genotypes CCN51 and TSH565 using 13 SSR. The leaves of in vitro plantlets (IVL) were collected from 6-month-old plants and leaves of field plants (FPL) were selected from 3-year-old trees. The 13 analyzed loci revealed 25 alleles in genotype CCN51 and 24 alleles in genotype TSH565. The highest PIC value was observed for all SSR, only mTcCIR8 and mTcUNICAMP09 were intermediate, with PIC values of less than 0.250. IVL and FPL populations were genetically equal. According to the results, no differences in allelic composition were observed between FPL and IVL in each genotype. This indicates that plants propagated by SE did not show perceptible detriment to their genome with the used SSR. In addition, Jaccard's coefficient showed more than a 91% similarity for TSH565 and 92% for CCN51. The UPGMA and PCA showed that the populations tended to group within two genotypes. The SSR results obtained do not exclude the occurrence of other changes in the nuclear genome. However, considering the morphological stability of in vitro propagated plants, the results indicate that the protocol used is suitable and efficient for large scale, true-to-type propagation of genotypes CCN51 and TSH565 for commercial purposes.