As an endemic economic shrimp along the coast of China, the ridge-tailed white shrimp Exopalaemon carinicauda has biological advantages such as strong reproductive ability, environmental adaptability, and a fast growth cycle. To investigate the genetic variation of different geographic populations of E. carinicauda in the China sea, we set up two spatial sequence samples, including 3 small-scale sequence samples (northern Zhejiang, central Zhejiang, and southern Zhejiang) and 5 large-scale sequence samples [Bohai Sea, Yellow Sea, East China Sea (Zhejiang), East China Sea (Fujian), and South China Sea]. These samples underwent PCR product purification and sequencing and a total of 210 samples of E. carinicauda from seven wild populations were sequenced for CO I and 16S rRNA gene sequences. The CO I gene sequence of 515 bps with 58.65% A+T content and the 16S rRNA gene sequence of 520 bps with 62.02% A+T content were obtained and the analysis results of two gene sequences in population genetic diversity were consistent with those of the Yellow Sea population having the highest genetic diversity and the population from the South China Sea having the lowest genetic diversity. The results of AMOVA analysis were consistent. The differences between the two gene sequence analyses were as follows: the CO I gene sequence analysis detected 63 variable sites, with a haplotype diversity (Hd) of 0.353–0.809 and a nucleotide diversity (Pi) of 0.00140–0.00497, while the 16S rRNA gene sequence analysis detected 41 variable sites, with an Hd of 0.265–0.801 and a Pi of 0.00102–0.00403. The CO I gene showed greater variation and was able to discriminate between samples in smaller-scale spatial sequences. The results of the present study provide basic data for the conservation of Exopalaemon carinicauda germplasm resources.