A total of 45 quinolone-resistant foodborne Salmonella isolates were used to screen for mutations in the parC and gyrA genes by whole-genome sequencing (WGS) and real-time polymerase chain reaction (real-time PCR). The reliability of the detection methods was tested, and the mutation characteristics of the antibiotic-resistance genes were evaluated. Four strains were subjected to next-generation WGS, and according to the results obtained, a real-time PCR assay was developed to detect the mutation sites of Asp87Tyr and Asp87Asn in gyrA, and Thr57Ser and Ser80Ile in parC. The Salmonella isolates were subjected to PCR detection for the qnrS, qnrA and qnrB genes. Thirty-one strains which were not found to carry the qnr genes were screened for mutation sites by real-time PCR, revealing that mutations of parC Thr57Ser and gyrA Asp87Asn were found to be the most frequent mutations. In order to check the accuracy of real-time PCR, PCR amplification of the complete sequences of gyrA and parC was performed on 10 positive strains and the resulting amplicons were sequenced. The sequencing results were completely consistent with the real-time PCR results. The combination of WGS and real-time PCR, which can be used to detect new mutations in genes conferring quinolone resistance and rapidly screen for the main type of mutation in massive samples, is a rapid and reliable method for the identification of gyrA and parC mutations in Salmonella.