[Objectives] The Red-crowned Crane (Grus japonensis) is listed as a National Class I Key Protected Species in China and evaluated as Vulnerable (VU) by the International Union for Conservation of Nature (IUCN). It has maintained a small wild population in China due to the deterioration of its natural habitats. As an important migratory stopover site and the second-largest wintering ground for this species in China, the Yellow River Delta has witnessed a continuous increase in its wintering population size in recent years. Understanding the genetic characteristics and diversity of this population is crucial for implementing effective conservation strategies. [Methods] We employed a non-invasive sampling method to collect 264 fecal samples of Red-crowned Cranes from the Yellow River Delta National Nature Reserve from December 2021 to February 2022 (Fig. 1), and extracted DNA from 127 samples. Individual identification and genetic diversity assessment were conducted based on seven microsatellite loci and the mitochondrial Cyt b gene. CERVUS 3.0 was utilized for individual identification and calculation of genetic diversity parameters, including the effective number of alleles (N_e), observed heterozygosity (H_O), expected heterozygosity (H_E), polymorphism information content (PIC), and Hardy-Weinberg equilibrium (HWE). GenAlEx V6.51b2 was used to quantify private alleles, inbreeding coefficient (F_IS), probability of identity (PID), and probability of identity among siblings (PIDsib). The population genetic structure was analyzed via Structure 2.3.4, and the genetic differentiation index (F_ST) and gene flow (N_m) between populations were calculated. Mitochondrial genetic diversity analysis was performed with DNASP 5.0 to calculate haplotype diversity (H_d) and nucleotide diversity (P_i). A median-joining haplotype network was constructed by POPART 1.7. [Results] Individual identification confirmed that 127 samples originated from 115 distinct individuals (Fig. 2). A total of 60 microsatellite alleles were detected, with N_e ranging from 1.640 to 6.414. The population exhibited low genetic diversity, with H_O, PIC, and H_E values of 0.617, 0.578, and 0.628, respectively. Its expected heterozygosity was significantly lower than that of the Zhalong population (P = 0.002), but not significantly different from those of the Yancheng and Hokkaido wintering populations (P > 0.05; Tables 2 and 4). The population showed a high inbreeding coefficient (F_IS = 0.128). Cyt b gene sequences were successfully amplified from 53 samples, revealing 13 variable sites and 12 distinct haplotypes. Haplotype diversity (H_d = 0.756) and nucleotide diversity (P_i = 0.001 92) indicated low genetic diversity (P_i < 0.005). Microsatellite-based population structure analysis divided the population into four subpopulations, while the genetic differentiation was minimal (F_ST 0.020 ~ 0.056, N_m 4.198 ~ 12.329; Figs. 3 and 4, Table 3). The haplotype network constructed from Cyt b sequences showed no significant intraspecific genetic differentiation (Fig. 5). [Conclusion] These findings suggest that the wintering population in the Yellow River Delta exhibits low genetic diversity and a relatively homogeneous genetic structure. This study pioneers the use of fecal DNA for individual identification and genetic analysis in wild Red-crowned Cranes, providing a methodological application for genetic diversity assessments for wild Red-crowned Crane populations and other endangered species.