In recent years, mitochondrial diversity of goats has been extensively studied, in order to shed light on domestication processes. There are limited studies on genetic diversity and demographic history of Anatolian goat breeds, and these studies have focused only on modern goats. Until today, no research has been conducted on DNA analysis of ancient Anatolian goats. In the present study, seven ancient DNA samples of goat remains from Van‐Yoncatepe archaeological site in Eastern Anatolia, Turkey, dating 1000 BC, were successfully extracted and amplified for the first time. A 230‐bp fragment of mitochondrial DNA Hypervariable Region 1 of the samples was analyzed. All of the ancient sequences belonged to haplogroup A, which is the most widely distributed and frequently encountered haplogroup in modern goats. The results also pointed out that Anatolian ancient goats might have contributed to the genetic structure of modern goats in the Near East, the Mediterranean Region and South‐Southeastern Asia. Copyright © 2014 John Wiley & Sons, Ltd.