The nuclear ribosomal RNA (nrRNA) genes of eukaryotes are organized in clusters of tandem repeat units, including three genes (18S, 5.8S, and 28S) and two internal transcribed spacers (ITS1 and ITS2). The ITS2 is located between the 5.8S and 28S genes. Because multiple copies of ITS2 have different intra-and inter-species evolution rates, ITS2 is often used as the molecular marker to identify species or to infer the phylogenetic relationship at the rank of species or genera. In this study, 11 species from five families of Perciformes were selected as the representatives to investigate the characteristics and the evolutionary pattern of the ITS2 in fishes. A total of 444 cloning sequences of ITS2 were obtained from 24 samples through PCR and cloning methods. The length of these sequences ranged between 332-515 bp. A comparison of sequences within species found that the length of (32 bp) were extremely varied, and that of others, less than 14 bp, were relatively conservative. The evolutionary pattern of ITS2 of 11 species within species were conjectured based on the difference in several polymorphism characteristics, including the difference in length, conserved and variable sites, parsimony-informative site, the number of haploid type, proportion of conserved and variable sites, haploid type diversity index, nucleotide diversity and genetic diversity. The two out of 11 species () had obvious differences, especially the three different sequence types (Type A, Type B and Type C) detected in three individuals, suggesting a non-concerted evolution. Although, to a certain extent, length and variable sites were observed in four other species (, and S. leptolepis and , therefore, the four species were not subjected to strict concerted evolution (no-strict concerted evolution). The five other species (Toxotes chatareus, and ) almost had no intraspecific variations, suggesting a concerted evolution process. Meanwhile, there was no correlation between the evolution pattern of 11 species and the taxonomic system. In addition, sequence comparison revealed that transitive sequences between concerted evolution and non-concerted evolution were observed in , all three evolutionary patterns (concerted evolution, no-strict concerted evolution and non-concerted evolution) were detected in three individuals. Based on 444 cloning sequences of ITS2 from 11 species with as the outgroup, two phylogenetic trees were constructed using the neighborjoining and maximum likelihood methods. The results showed that both trees were largely congruent with each other. The topology showed that sequences from the same species clustered together and sequences from each genus of seven genera in Carangidae claded together. These results supported that the ITS2 is applicable as a molecular marker for species identification, but also useful for phylogenetic relation analysis at the rank of genus in Carangidae.