Abstract: In order to obtain the parasitics and population genetic structure of Anisakis pegreffii in Coilia nasus and deeply understand its marine life background, three sampling areas were set up as Chongming, Taizhou, and Anqing sections in the lower reaches of Yangtze River.. A total of 15 fish were sampled during the early, middle, and late fishing season of different river sections from April to July in 2021. The A. pegreffii parasitized in C. nasus was identified and its population genetic structure was analyzed using a molecular marker of ITS region. Results showed that totally 354 A. pegreffii were identified from 135samples, the infection rate of A. pegreffii was 77.78%, with an average infection intensity of 3.37±2.97 individuals per fish and an average infection abundance of 2.62±2.97 individuals per fish. ,In terms of time characteristics, the highest infection rate (86.67%) occurred during the early fishing season, which was significantly higher than that in the middle (75.56%) and late fishing season (71.11%). And the highest infection intensity (5.27±3.96 individuals per fish) was observed in late investigation, which was significantly higher than that in the early (3.07±3.13 individuals per fish) and middle (3.01±2.21 individuals per fish) investigation (P<0.05). However, there was no significance for the infection abundance among three different periods. In terms of spatial characteristics, both the average of infection intensity and infection abundance of A. pegreffii were the maximum in Anqing segment reached as 4.83 and 4.29 individuals per fish respectively, which showed extremely significant (P<0.01) compared to Taizhou and Chongming segments. Correspondingly, the lowest values were observed in Taizhou segment, with no significant difference compared to Chongming. For genetic structure analysis, totally 369 polymorphic loci were screened, in which 6single information loci and 363 reduced information loci were found. Furthermore, twenty-three haplotypes were identified and Hap_1 and Hap_2 were the dominant haplotypes. Haplotype diversity index (H_d), nucleotide diversity index (π) and average nucleotide difference number (K) were synchronously analyzed and the value reached as 0.523, 0.23633 and 162.123 respectively. The haplotype phylogenetic tree based on ML and NJ method showed that A. pegreffii in C. nasus originated from two lineages, and genetic differentiation was significant between two lineages (F_st=0.98946, P<0.01) through AMOVA analysis. Finally, Mismatch analysis and neutrality test also indicated the two lineages experienced a significantly population expansion in recent.