Abstract: Silver carp is one of important breeding fish in China. It is necessary to study the growth traits markers to accelerate the molecular marker-assisted breeding techniques. The simple sequence repeat (SSR) from the transcriptome of egg in silver carp were characterized by high-throughput Illumina sequencing, and genotypes associated growth traits were analyzed. The main results are as follows: (1) 77129 unigenes were detected by assembly, 31.7% of 24458 ESTs contained repeat motifs of various types (dinucleotide, trinucleotide, tetranucleotide and pentanucleotide) and lengths with AC being the most abundant dinucleotides one. (2) 175 EST-SSR primers were randomly characterized and 36 polymorphic EST-SSR were developed in silver carp. The results of Blast indicated that 10 EST-SSR genes are known. (3) The results showed that two loci were significantly correlated with growth traits in full-sibling family in silver carp. One locus SCE26 was significantly (P<0.05) correlated with body length and body weight, and SCE65 was significantly (P<0.05) correlated with condition factor. This study will provide theoretical basis and technical methods for the development of the marker-assisted breeding system in silver carp.