Hybrid dandelions between introduced and native dandelions have been spreading in Japan. There are multiple lineages of hybrids, but their origins and expansion processes are unknown. We expect the geographical origins of hybrids to be detected by comparing cpDNA sequences between hybrids and natives because cpDNA of hybrids are always derived from natives. In this study, we collected native and hybrid samples over the distribution area of native species and compared their cpDNA sequences. There were two major haplotypes shared between natives and some triploid hybrids. Their distributions were divided into western and central-eastern Japan both for natives and hybrids, indicating that these hybrids did not expand their distribution outside of the original areas at this spatial scale. However, we could not specify the origins of other hybrids because some triploid hybrids shared a haplotype spreading over the sample area in natives and because the haplotype of most tetraploid hybrids was not found from natives. We, therefore, tried the 'GRAS-Di' method, which collected genome-wide variations with a NGS as a finer resolution genetic marker. The GRAS-Di solved finer scale geographic variation in native species suggesting a possibility to be used as a marker for detecting hybrid origin.