In order to study the genetic diversity and genetic structure of the natural population of Neocaridina palmata, DNA barcode technology was used to amplify, sequence and analyz of mitochondrial COⅠ gene fragments from 97 samples in 7 wild populations(Qingyuan, Huizhou, Shaoguan, Guangzhou, Hechi, Nanning and Chongzuo). The results showed that the average content of A, T, C and G bases in the 624 bp COⅠ gene sequence of Neocaridina palmata in the Guangdong and Guangxi region were 26.98%, 33.17%, 20.99% and 18.85%, respectively, showing a greater preference for A and T base with the AT content(60.15%) and GC conent(39.84%). A total of 4 polymorphic sites and 5 haplotypes were identified in the total population based on COⅠ gene sequence. Moreover, the average number of nucleotide differences(K), haplotype diversity(Hd) and nucleotide diversity(Pi) were 0.611, (0.557±0.025) and (0.000 98± 0.000 07), respectively, indicating high haplotype diversity and low nucleotide diversity. The genetic distance within the population of 7 natural populations was 0.000–0.001, and the genetic distance between populations was 0.000–0.002. Analysis of molecular variance(AMOVA) and genetic fixationindex(Fst) revealed that the genetic variance of N. palmata was mainly from the population. The neutral test and nucleotide mismatch distribution indicated that the seven N. palmata did follow the population expansion pattern and had ever experienced population expansion. Phylogenetic analysis showed that the Guangdong 4 population and the Guangxi 3 population formed a sister branch, indicating that different geographical regions have certain their own population characteristics and can be used to protect separate management units. In addition, Hap1 and Hap4 were shared haplotypes of Guangdong 4 populations, Guangxi 3 populations and Huizhou population, respectively, and the remaining haplotypes are exclusive to each population.