These raw data belong to the paper published in the Journal of Biogeography: Jiang et al. (2021) Shifting roles of the East China Sea in the phylogeography of Machilus thunbergii (Lauraceae) in East Asia. Journal of Biogeography. Any questions about the raw data, please contact the author (Kai Jiang, jiangkai@csnbgsh.cn). There are two files containing the species distribution locations and microsatellite genotype data, respectively. In the file of Coordinates_of_Machilus_thunbergii.csv, three columns can be found: The first column is the species name, the second is longitude, and the third is latitude. In the file of raw_microsatellite_genotypes.xlsx, eighteen columns and 641 lines can be found: The first line is the head, including the POP, IND, and locus name. From the second line to the end, every line shows a single individual with nine loci (18 alleles). The first column is the population name, and the second is the individual name. From the third and eighteen columns, the same locus shares the same name. Each locus has two alleles because Machilus thunbergii is a diploid species. The blank represent the missing data.