The New World is the last continent colonized by anatomically modern humans, Homo sapiens. The first migrants entered the New World from Asia through Beringia. It is suggested that there were three streams of Asian gene flow, one major and two additional minor gene flows. The first major migrants took a Pacific coastal route and began spreading to the American continent before the opening of the ice-free corridor. We investigated the diversity of full-length mitochondrial DNA genomes of the Zapotec population, residing in the Mesoamerican region, and reconstructed their demographic history using Bayesian Skyline Plots. We estimated the initial date of gene flow into the New World by Zapotec ancestors at around 17 000-19 000 years ago, which is highly concordant with previous studies. We also show a population decline after the initial expansion. This decline started 4000 years ago, long before European contact with Native Americans. This indicates that other factors including climate change should be considered to explain the observed demographic pattern.