Intraspecific diversity of molluscan species is usually studied based on maternally inherited mitochondrial DNA, from which only part of the evolutionary history can be reflected. Some nuclear ribosomal RNA genes such as 28S rRNA represent poten- tial candidates that can be easily applied in phylogeography because of lacking intraindividual variation. However, considering their low polymorphism, genetic appraisals on whether and how they can be used in population studies are necessary. Here, we applied a short 28S rRNA to assess genetic patterns of the clam Cyclina sinensis along the coast of China and compared the results with a for- mer study based on COI and ITS-1 analyses. The results revealed the 28S rRNA data set was characterized by an extremely low level of variation, with only seven haplotypes defined for 93 individuals. Haplotype and nucleotide diversity for each population was al- most the lowest when compared with the other two markers. However, the distribution of two dominant haplotypes showed clear geo- graphic patterns, and significant population differentiation was revealed between the East China Sea and the South China Sea. These patterns were highly concordant with findings of the former study that populations of C. sinensis were historically separated by land bridges among sea basins. Our study suggested that although the nuclear rRNAs have shortcomings such as low variation, they have advantages including lack of intraindividual variation and high amplification rates. Applying rRNA genes can enrich the toolbox of nuclear markers in molluscan phylogeographic studies.