The ribosomal RNA gene (rDNA) cluster consists of multiple units of three coding genes (18S, 5.8S, and 28S) as well as two internal transcribed spacers (ITS1 and ITS2) separating the coding regions. Thus far, studies on these five fragments mainly focused on the polymorphism of different copies within each individual sample and identification of useful markers for phylogenetic relationship analysis. However, there are limited studies related to the features of GC content, which is a very important characteristic of ribosomal RNA gene. The characteristics of rDNA GC content and whether the GC balance phenomenon exists in the coding regions in fishes were investigated by selecting 11 species from five families of Perciformes, including Latidae, Toxotidae, Rachycentridae, Xiphiidae, and Carangidae. In all, 1651 monoclones from the five fragments mentioned above were obtained. The GC content features were analyzed based on the sequences from the 11 species or the datasets from other teleostean fishes retrieved from GenBank. The results from the above two analyses were compared. The following results were obtained. First, the GC content of 18S, 5.8S, 28S, ITS1, and ITS2 ranged from 52.6% to 57.1% (average, 54.6%), 55.6% to 58.9% (average, 57.4%), 64.2% to 65.8% (average, 64.6%), 56.5% to 73.0% (average, 65.0%), and 62.3% to 77.5% (average, 69.1%), respectively. Second, compared with non-coding regions, coding regions were relatively conserved. The GC content of the coding genes varied in smaller ranges than those of the internal transcribed spacers. The GC contents of 18S and 5.8S were lower than those of ITS1 and ITS2, but that of 28S was between the lowest and highest values of ITS1 and ITS2. Therefore, we found that the GC content of non-coding regions was higher than 60%, which was a remarkable characteristic of these fishes, and no correlation was found between fragment length and higher GC content. Further, no obvious G, C, or GC rich block was found in the high-GC-content regions of ITS1 and ITS2 sequences. Third, the similarity of GC content between ITS1 and ITS2 within the same species could be higher or lower than that of the same fragment among different species within the 11 species. Therefore, the GC balance phenomenon is not universal and only exists in species whose intra-species GC content similarity is lower than the inter-species GC content similarity. The results of this study might provide a scientific basis for further studies and facilitate the utilization of the ribosomal gene characteristics of fish.