Dill (Anethum graveolens L.) is an annual herb with a long history and it is mainly used as a spice and as a medicine that is effective as a digestive aid, a sedative, and a narcotic, and that helps remove bad breath. Dill grows wild in the districts along the shores of the Mediterranean Sea, West Asia, China, and Korea. An estimate of the phylogenetic relationships within dill accessions in 20 countries was inferred using data from the rps16-trnK3-intergenic spacer. The aligned data sets for dill ranged from 747 to 779 nucleotides (bp) as a result of the differences in the insert/delete nucleotides. The sequence variation within the dill accessions was mostly due to nucleotide substitutions, although several small insertions and deletions can be found. Among 100 accessions from 20 countries, the Eastern Asia accessions were more closely related to the North American accessions than to the Central Asia and European accessions. Although some accessions were not congruent completely with geographical locations, the dill accessions with rps16-trnK analysis resulted in plants with better-resolved clades.