Comparative transcriptomics data have become one of the most important ways to study single nucleotide polymorphisms (SNP). We have identified 129 gene segments associated with growth. SNP is a third-generation mo- lecular marker and is useful for breeding rapidly growing species, such as the swimming crab, Portunus trituberculatus. We developed an efficient method to selectSNPs correlated with P. trituberculatus growth. Time-of-flight-mass spec- trometry was used for SNP typing, and the chi-square test was used for the correlation analysis. Nineteen gene segments were amplified based on comparative transcriptomics, and a total of 17 387 bp DNA fragments were amplified. SNP frequency was estimated to be 0.43/100 bp of DNA sequence, the conversion mutation rate was 80%, and the transver- sion mutation rate was 20%. The conversion ratio was far greater than the transversion ratio to comply with the princi- ple of “transition bias”. The G/T (C/A) rate was 20%, the A/T rate was 9.33%, the G/C rate was 10.67%, and the C/T (G/A), which is the most common gene mutation type, was 60%. The intron mutation frequency was 1.34/100 bp and that of exons was 0.17/100 bp, indicating that the exon mutation frequency was more conserved. Three SNP markers were significantly correlated with growth traits, and P-values of 10 SNPs were < 0.05. The chi-square test result re- vealed that comp58070-R31 was closely related to growth traits (P<0.01). A multivariate analysis of variance showed that comp58070-R31 was closely related to body weight, full carapace width, and carapace width (P<0.01). A signifi- cant correlation was detected between body length and body height(P<0.01). Loci comp46623-F49 and comp49193-R333 were significantly correlated with carapace width (P≤0.05). Observed heterozygosity of the P. trituberculatus SNPs was 0.162 8–0.833 3, and expected heterozygosity was 0.189 6–0.591 2, indicating less information content than that from microsatellite markers. These SNPs will be helpful for pedigree analysis, association studies, and marker-associated selection in this crab species.