The chloroplast DNA (ctDNA) type was determined for most of Japanese potato varieties including both officially registered and unregistered varieties and those of unknown origin. Many modern varieties have T type ctDNA similar to the present European potatoes. Some varieties have W type ctDNA which was derived from S. demissum. Most of varieties of unknown origin have T type ctDNA. It indicates those were introduced after late blight epidemics in Europe and/or bred from them. Four old varieties have A type ctDNA which is typical to Andean potatoes and has been found in a derivative of the oldest European variety, Myatt's Ashleaf. Considering the historical background in Japanese potatoes, it is suggested that these old varieties are relic potatoes of the early European potato and similar ctDNA introduction and incorporation occurred in both Europe and Japan.