Mitochondrial hypervariable region I genetic data from ancient populations at two sites in Asia—Linzi in Shandong (northern China) and Egyin Gol in Mongolia—were reanalyzed to detect population affinities. Data from 51 modern populations were used to generate distance measures (F_ST's) to the two ancient populations. The tests first analyzed relationships at the regional level and then compiled the top regional matches for an overall comparison to the two probe populations. The reanalysis showed that the Egyin Gol and Linzi populations have clear distinctions in genetic affinity. The Egyin Gol population as a whole appears to bear close affinities with modern populations of northern East Asia. The Linzi population seems to have some genetic affinities with the West, as suggested by the original analysis, although the original attribution of “European-like” seems to be misleading. We suggest that the Linzi individuals are potentially related to early Iranians, who are thought to have been widespread in parts of Central Eurasia and the steppe regions in the first millennium b.c., although some significant admixture between a number of populations of varying origin cannot be ruled out. We also examine the effect of sequence length on this type of genetic data analysis and discuss the results of previous studies on the Linzi sample.