The first and second internal transcribed spacer (ITS1 and ITS2) regions of the ribosomal DNA from six species, Meretrix meretrix, Cyclina sinensis, Mercenaria mercenaria, Protothaca jedoensis, Dosinia corrugata and Ruditapes philippinarum, in the family Veneridae were PCR amplified and sequenced. The size of the ITS1 sequence ranged from 522–900 bp, which was the largest range so far reported for a bivalve species, with GC contents from 57.66% to 65.62%. The size of the ITS2 sequence ranged from 281–412 bp, with GC contents from 65.21% to 67.87%. Extensive sequence variation and obvious length polymorphisms were noted for both regions in these species, and ITS2 sequence similarity was higher than that of ITS1 across species. The complete sequences of 5.8S ribosomal RNA gene were obtained by assembling ITS1 and ITS2 sequences, and the sequence length in all species was 157 bp. The phylogenetic tree of Veneridae clams was reconstructed by using ITS2 containing partial sequences of both 5.8S and 28S rDNA, and corresponding sequence information in Arctica islandica (Dahlgren et al. 2000) as an outgroup species. Tree topologies indicated that P. jedoensis has a closer relationship with M. mercenaria than with other species.