The yak (Bos grunniens) is an indigenous domestic animal living at high altitudes in the Tibetan plateau that is economically important for the Tibetan people. In this study, we investigated the diversity and phylogeography of four geographic ecotype populations of the Naqu yak (133 individuals) using an 811-bp mitochondrial DNA D-loop region sequence. In total, 57 polymorphic sites, including 54 single-nucleotide polymorphisms and 3 single-nucleotide copy number variants, and 59 haplotypes were detected. The number of haplotypes within the population ranged from 17 (SN and JL) to 28 (DX). The haplotype diversity ranged from 0.9420 (SN) to 0.9770 (NR). The highest nucleotide diversity was found in the JL population (0.01479), whereas the lowest was found in the SN (0.00894) population. Phylogenetic analysis revealed that these four populations separated into two haplogroups; the first included SN, DX, and NR, and the second included JL. However, no significant divergence was found among the ecotype populations using a pair-wise difference comparison (FST). Thus, the Naqu yak has multiple maternal origins and demonstrates high diversity within 4 geographic ecotype yak populations. In addition, the yaks exhibit some diversity based on the number of unique haplotypes within each population; however, they have not heavily and significantly diverged because all the populations share the most high-frequency haplotypes. Therefore, this study not only shows that the different ecotype populations of the Naqu yak carry high genetic diversity but also indicates that frequent genetic material exchanges have led to smaller differences in genetic divergence between different ecotypes.