The class Bivalvia(phylum Mollusca) is a morphologically and ecologically diverse group that inhabits a variety of marine environments. Worldwide, there are approximately 20,000 species of marine bivalves that display a rich genetic diversity. Clear and reliable evolutionary relationship information is important for the culture and management of related species. Recently, it has been shown that comparative phylogenetic analyses based on small subunit rRNA gene(18S) sequences may be useful for resolving phylogenetic relationships within and among bivalve families. However, a comprehensive examination of bivalves is lacking so far. In this paper, 18S nucleotide variations were analyzed and used to investigate the evolutionary relationships among 3 subclasses of the Bivalvia. 18S sequences of ninety-four species, which belongs to six orders, were obtained from GenBank. Sequences were aligned by using the profile alignment function of ClustalX, and regions which could not be unambiguously aligned were excluded. The phylogenetic analyses were conducted using the Neighbor-Joining method(in MEGA 4.1) and the maximum likelihood method(in PHyML). The alignment results showed that many indels(insertions/deletions) were observed, so there is polymorphism in sequence length of these sequences. The 18S alignments for the 107 sequences contained 1796 sites in total, comprising 569 variable sites(31.7%) and 431 informative sites(24.0%). We observed 5 regions of highly conserved sequences and 4 regions of high variability. The mean composition of T, C, A, G, was 24.4%, 23.6%, 24.5%, 27.5%, respectively, and this dataset shows a higher proportion of G in all 18S sequences. Genetic distances among families and among orders were from 0.003 to 0.043 and from 0.026 to 0.093, respectively. The present analysis of the 18S data supports the proposal that each of the following 4 orders forms a distinct clade: Arcoida, Nucubida, Mytiloida and Pterioida. The monophyly of each order is supported by a relatively high bootstrap value(BPN=94 100). NJ and ML trees supports the placement of orders Arcoida, Nucubida, Mytiloida and Pterioida in one clade(BPN=100, and clustered with the family Hiatellidae(Order Myoida)(BPN=97). The Veneroida and Myoida were not recovered as monophyletic clade. In the case of the order Veneroida, the species of the family Mactridae grouped closest to one another(BPN=98) but separate from the other species of Veneroida. The Veneroidae clustered as a monophyletic clade with lower confidence level(BPN=60), and the species of the family Hiatellidae separate from the order Myoida. The Mactridae and Hiatellidae each formed a monophyletic clade.