Objective Lactase persistence (LP) is an adaptive trait that certain human populations have acquired in response to lactose consumption in adulthood. The T‐13910 variant has been reported as a causal polymorphism in Europeans. The Ecuadorian population has been described as multicultural and multiethnic, comprised of three main ethnic groups (Mestizo, Native Amerindian, and Afro‐Ecuadorian). The aim of the study was to identify the molecular basis of LP in these admixed populations for the first time and determine the association between the T‐13910 marker and the European ancestry proportion of each ethnic group. Methods Genotyping was performed in 741 Ecuadorian individuals by sequencing a 576 bp region around the ‐13910 position upstream of the LCT gene. The ancestry proportions of Mestizo, Afro‐Ecuadorian, and Native Amerindians were calculated using Ancestry Informative Markers and were compared with the diversity panel of the Human Genome Diversity Project. Results LP prevalence calculated from T‐13910 allele frequency in Mestizo, Afro‐Ecuadorian, and Native Amerindians was 24.4%, 16%, and 12.5%, respectively. The ancestry percentage correlated to the admixture proportion of each ethnic group, and the C/T‐13910 genotype frequency was influenced by the European ancestry proportion. Conclusions The presence of the T‐13910 polymorphism in the Ecuadorian population suggested that LP was a trait introduced by European migration and inherited by admixture that occurred during the colonization of South America. This variant was not fixed in a population with a history of admixture, and its allele frequency was proportional to the ancestry proportion of each Ecuadorian ethnic group. Am. J. Hum. Biol. 28:774–781, 2016. © 2016Wiley Periodicals, Inc.