Three main ethnic groups live in the South American country of Ecuador: Mestizos, Amerindian natives, and African-derived populations, or Afro-Ecuadorans. Mestizos and Afro-Ecuadorans can be considered trihybrid populations containing genes originating in the Americas, Europe, and Africa, as is the case with equivalent populations in other Latin American countries. The proportion and the dynamics of the admixture process remain unknown. However, a certain sex asymmetry of the admixture process can be expected for historical reasons. We typed 11 Y-chromosome short tandem repeats (STRs) in these three ethnic groups to provide adequate allele and haplotype frequencies for forensic genetic purposes and to quantify admixture proportions in male lineages. In addition, a data set of 15 autosomal STRs in the same samples were reanalyzed for the same purpose. Contributions to Mestizo Y chromosomes were estimated to be 70% European, 28% Amerindian, and 2% African, whereas in autosomes the contributions were 19%, 73%, and 8%, respectively, which underlines the sexual asymmetry in mating, with Europeans contributing mostly males. European Y-chromosome haplotypes in Mestizos were similar to those in Spain. Moreover, about 10% of European Y chromosomes were found in the Amerindian Kichwa. As for Afro-Ecuadorans, their contributions to the male line are 44% African, 31% European, and 15% Native American; the last value is the highest percentage reported so far for an African-derived American group. Autosomal admixture was estimated as 56% African, 16% European, and 28% Amerindian.