Single nucleotide polymorphisms (SNPs) are the most dominant type of DNA variations in genome which is useful in genetic linkage mapping and quantitative traits loci analysis. In this study, a SNP's database of blunt snout bream (Megalobrama amblycephala) was obtained from the transcripts of cDNA library using Solexa/Illumina sequencing. A total of 36,326 putative SNPs were discovered from the transcripts. One SNP was found in 29.2 base pair length of the transcripts. The transition and transversion mutation was 21,445 and 12,553 SNPs, respectively. A ratio of transition to transversion was 1.71. Within those yielded SNPs, 10,812 SNPs identified from 2,421 unigenes could be annotated to differential functionality in comparing to public database using BLASTX for gene ontology (GO), eukaryotic orthologous groups of proteins (KOG), and Kyoto encyclopedia of genes and genomes (KEGG). A number of SNPs (n = 7,727, 71.5%) found from 1,628 unigenes were assigned to three main GO categories: 'cellular components', 'molecular function' and 'biology process'. In total, 5,812 SNPs (53.8%) identified from 1,324 unigenes were classified into 25 KOG categories. 4,589 SNPs (42.4%) detected from 975 unigenes were assigned to 278 KEGG pathways. Furthermore, a number of 600 SNPs found from 111 unigenes were successfully annotated in the term 'immune system' via KEGG classification. The SNP's database in this study could be useful for further genetic studies in blunt snout bream.