Scallops are a cosmopolitan family, found in all of the worlds oceans.They are a major grouping of the bivalves which in turn constitute the second largest group of mollusks.Studies of scallop phylogeny are mainly based on morphological characters and very limited molecular data so far, and have never come to a genome level.Fortunately, the recent advent of high-throughput sequencing platforms provides the turning point for scallop research,which can dramatically speed up genetic or genomic studies in potentially any non-model organisms.Here we applied a recent developed type Ⅱ B enzyme based tags sequencing technology that allows comprehensive polymorphism data to be utilized, to six scallop species (C.farreri, P.yessoensis C.nobilis, A.irradians, A.purpuratus, and P.magellanicus), hoping to look into their phylogenomic relationships.In a full plate of Illumina sequencing run, more than 150 million high quality tags with eighty-fold average sequencing coverage were produced.A cluster-derived reference was generated with these tags using CD-HIT program.Conserved tags between the six scallop species and genome-wide single nucleotide polymorphisms (SNPs) were identified by mapping the full set of reads against the reference.The SNP calling process is still in progress right now, and a phylogenomic network will be constructed to describe the relationships between the six scallop species and facilitate inferences concerning the speciation and diversification of scallops.