In order to identify genes associated with growth traits and SNP (Single nucleotide polymorphism) markers in Ctenopharyngodon idella, RNA-Seq (RNA Sequencing technology) was used to analyze the transcriptomes of liver, muscle and brain tissues of fast-growing and slow-growing C. idella groups. A total of 314.65 million clean reads were gained for the fast-growing and slow-growing groups, and 34 147 unigenes were assembled, with an average length of 1 060 bp, of which 30 751 genes were annotated. 1 013, 552, and 372 significant differentially expressed genes were screened in liver, muscle, and brain tissues, respectively, of which 4 580 SNP markers were detected. Then, the polymorphisms of 34 SNP markers was detected and validated with SNaPshot technique in the extreme populations of growth traits of C. idella (n=300), and among which, 30 SNPs (83.24%) were successfully genotyped. A general linear model was used to analyze the correlation between 30 SNPs and growth traits. The results showed that at the position of Unigene00810126-8014, the body weight, body length, body height, head length and caudal peduncle length in individuals with CC genotype had significantly higher values than TT genotype. At the position of Unigene00810126-2903, the body weight of AA genotype was significantly higher than those with GG genotype. At the position of Unigene00870394-525, individuals with the AA genotype had significantly higher values in body weight and body height than those with GG genotype. At the position of Unigene02938762-011628, TT and CC genotypes had significant differences in body mass, body length and head length traits. Besides, other SNPs loci were not significantly correlated with growth traits. The four selected markers were located at Somatolactin alpha (slα), Early growth response protein-1 (egr-1) and Myosin heavy chain (myh) genes. The average polymorphism information content (PIC), average expected heterozygosity (H_e) and average observed heterozygosity(H_o) of 8 EST-SNP markers in C. idella population were 0.300, 0.377 and 0.363, respectively, indicating that genetic diversity of C. idella breeding population had relatively high level. In conclusion, 1 937 differentially expressed genes and four SNP markers related to growth traits were obtained, which can be used as candidate genes and for molecular marker-assisted selection of C. idella, and can also be used in subsequent breeding work.