Ribosomal DNAs were mapped comparatively with fluorescence in situ hybridization (FISH) in Argyrosomus amoyensis and Larimichthys crocea to explore the variations of karyotype microstructure among Sciaenids. The results showed that the karyotypes were quite different between A. amoyensis and L. crocea referring to macrokaryotype, and distribution mode of 18S rDNAs and 5S rDNAs. In A. amoyensis, the karyotype is 2n=48t (FN=48); single pair of 18S rDNA signals were mapped at interstitial region of Chromosome 1; and single pair of 5S rDNA signals were located at proximal region of Chromosome 3. In L. crocea, the karyotype is 2n=2sm+4st+42t (FN=50); single pair of 18S rDNA signals were mapped at terminal region of short arm of Chromosome 18; and 9~11 pairs of 5S rDNA signals distributed mostly on centromeric termini of acrocentric chromosomes or terminal on the short arms. Together with the available cytogenetic data of Sciaenids, the following conclusions were drawn:(1) the karyotype of A. amoyensis represents characteristics of ancestral karyotype in Sciaenidae, while the karyoytpe of L. crocea was derived from the ancestral karyotype through rearrangement and transposition; (2) the macrokaryotype and the location of 18S rDNA sites were rather conservative in Sciaenidae with several exceptions, while the 5S rDNA sites varied dynamically among species. Hence, further studies to investigate microstructure variations of karyotypes among Sciaenid species with FISH should be encouraged.