Abstract: Twenty thermal-tolerant and twenty thermal-sensitive individuals of Larimichthys crocea were sequenced using specific-locus amplified fragment (SLAF-seq) technology based on Illumina HiSeq^TM2500 platform. 419211 SNPs were identified with an average read depth of 10.26× for each sample. Thirty-eight SNPs (P<2.39E–08) signifi- cantly related with thermal tolerance trait were identified according to association analysis. The SNP locations in large yellow croaker genome were identified using BLAST program, and functional genes around SNP were annotated. Twenty-six genes with known functions were discovered around 38 SNPs, which mainly regulate cell transcription, metabolism and immunity. These results provide basic information to analyze thermal-tolerant molecular mechanism and develop thermal-tolerant lines of Larimichthys crocea in the future.