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Background  Chinese grass shrimp ( Palaemonetes sinensis ) is an important species widely distributed throughout China, which is ecologically relevant and possesses ornamental and economic value. These organisms have experienced a sharp decline in population due to overfishing. Therefore interest in  P. sinensis  aquaculture has risen in an effort to alleviate fishing pressure on wild populations. Therefore, we investigated the genetic diversity and variation of  P. sinensis  to verify the accuracy of previous research results, as well as to assess the risk of diversity decline in wild populations and provide data for artificial breeding.    Methods   Palaemonetes sinensis  specimens from seven locations were collected and their genetic variability was assessed based on mitochondrial  COI  gene segments. DNA sequence polymorphisms for each population were estimated using DNASP 6.12. The demographic history and genetic variation were evaluated using Arlequin 3.11. At last, the pairwise genetic distance ( Ds ) values and dendrograms were constructed with the MEGA 11 software package.    Results  Our study obtained sequences from 325 individuals, and 41 haplotypes were identified among the populations. The haplotype diversity ( H   d  ) and nucleotide diversity ( π ) indices ranged from 0.244 ± 0.083 to 0.790 ± 0.048 and from 0.0004 ± 0.0001 to 0.0028 ± 0.0006, respectively. Haplotype network analyses identified haplotype Hap_1 as a potential maternal ancestral haplotype for the studied populations. AMOVA results indicated that genetic variations mainly occurred within populations (73.07%). Moreover, according to the maximum variation among groups ( F   CT  ), analysis of molecular variance using the optimal two-group scheme indicated that the maximum variation occurred among groups (53.36%). Neutrality and mismatch distribution tests suggested that  P. sinensis  underwent a recent population expansion. Consistent with the SAMOVA analysis and haplotype network analyses, the  D s and  F   ST   between the population pairs indicated that the JN population was distinctive from the others.    Conclusions  Our study conducted a comprehensive characterization of seven wild  P. sinensis  populations, and our findings elucidated highly significant differences within populations. The JN population was differentiated from the other six populations, as a result of long-term geographical separation. Overall, the present study provided a valuable basis for the management of genetic resources and a better understanding of the ecology and evolution of this species.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12862-021-01893-8.

Genetic diversity and variation of seven Chinese grass shrimp (Palaemonetes sinensis) populations based on the mitochondrial COI gene