Cacao is an economically important crop, since it provides the raw material for the multibillion dollar global chocolate industry. Yunnan Province is in the far southwestern region of China where tropical agriculture makes up a significant part of the provincial GDP. There is great potential for cacao production in Yunnan, given the rapid increase of chocolate consumption in China. Understanding the genetic background of available germplasm is essential for effective genebank management and crop genetic improvement. The objectives of this investigation were to assess the genetic identity of the cacao germplasm maintained in Yunnan, China; and to quantify the level of genetic diversity in comparison with available diversity in international collections. Using Single Nucleotide Polymorphism (SNP) markers, we genotyped the cacao collection maintained in the Xishuangbanna Tropical Botanical Garden in Yunnan. Multivariate analysis and Bayesian assignment test, using 150 reference cacao accessions, showed that these introduced cacao germplasm accessions have a narrow genetic background and were mostly comprised of Amelonado hybrids. Of the 88 Yunnan accessions, 59% of the parentage is contributed by Amelonado and 17% by two Upper Amazon Forastero populations. The study demonstrated that these introduced cacao germplasm accessions have a narrow genetic background thus lacking multiple sources of resistance to major cacao diseases. The present results therefore suggest that new introductions are needed to enrich genetic diversity in this collection. An improved germplasm collection would serve as a foundation for broader on-farm diversity for cacao cultivation in Yunnan, as well as in other tropical regions of China.