Purse red carp is an economic important and well-known domesticated variety of common carp in China. During a long history of domestication, purse red carp displays consumer-favored morphological traits such as red skin color and purse-shaped body form. However, the underlying genetic basis is less studied. In the present study, we utilized the powerful approach of comparative transcriptome analysis via high throughput sequencing, and examined transcriptome profiles of purse red carp by comparing with Yellow River carp, of which the skin color and body shape are quite similar to wild carp. A total of 434 million reads was generated, resulted in 203,590 assembled contigs, which was used as the reference sequences. Comparing the skin and blood transcriptome files showed that 2,767 unigenes were significantly differentially expressed, including 1,663 genes up-regulated and 1,806 down-regulated in purse red carp. Moreover, gene pathway analysis of the differentially expressed genes was conducted. We proposed the skin color and body shape depended upon at least four pathways including melanin biosynthesis, TGF-beta signaling, Wnt signaling and MAPK signaling pathways. We obtained candidate genes that may affect the morphological characteristics of purse red carp resulted from the long history of domestication, including TYRP1b, PMELa, KITa, BMP8a, ACVR2aa, TGFB1a, TGFB3, TGFBR2. Understanding the molecular mechanisms underlying the biological characteristics of purse red carp will advance our knowledge of the genetic differentiation between different common carp varieties caused by domestication, and accelerate the molecular selection of fish species with consumer-favored skin color and body shape.