Carnation is one of the most popular ornamental flowers worldwide. Due to its high ornamental and economic value, breeding techniques have advanced rapidly, leading to the continuous emergence of new varieties. However, this has also resulted in issues such as synonymy and homonymy. Therefore, utilizing DNA fingerprinting for rapid and accurate variety identification can play a crucial role in germplasm identification and the resolution of intellectual property disputes. In this study, we performed reduced-representation genome sequencing on 50 carnation accessions to develop single nucleotide polymorphism (SNP) markers. After filtering, 82,584 high-quality SNPs were obtained. These SNPs were used to conduct principal component analysis, population structure analysis, and cluster analysis on the 50 carnation accessions. From these high-quality SNPs, 130 SNP loci were further selected and converted into Kompetitive Allele-Specific PCR (KASP) markers. Preliminary screening using 92 carnation accessions yielded 53 KASP markers, and a subsequent screening with 217 carnation accessions identified 45 core KASP markers. Using these core markers, a fingerprint database was successfully constructed for 309 carnation accessions, achieving a distinguishing power of 99.987%. This study employed SNP fingerprinting and genetic analysis for the screening and identification of carnations, broadening the genetic basis at the molecular level and supporting subsequent variety protection efforts, thereby providing a scientific basis for carnation selection and identification.