Background: The Cuban population is essentially a result of the admixture between Spanish, West African and, to a lesser degree, Amerindian tribes that inhabited the island.

Aim: The study analysed the genetic structure of the three principal ethnic groups from Havana City, and the contribution of parental populations to its genetic pool.

Subjects and methods: According to genealogical information and anthropological traits, 206 subjects were classified as Mulatto, of Spanish decent or of African descent. Seventeen Ancestry Informative Markers, with high difference in frequency between parental populations, were selected to estimate individual and group admixture proportions. The statistical analyses were performed using the ADMIX, ADMIX95 and STRUCTURE 2.1 packages.

Results: The results demonstrate a high level of European and African admixture in Mulattos (57-59% European; 41-43% West African). The European contribution was higher in those of Spanish descent (85%) while in those of African descent, the West African contribution ranged between 74% and 76%. Genetic structure was only detected in Mulattos and those of African descent. An Amerindian contribution was not detectable in the studied sample.

Conclusion: Our findings indicate the existence of admixture and genetic structure in the population of Havana City. This study represents one of the first steps towards understanding Cuban population admixture in order to produce successful experimental designs for admixture mapping.