The class Scyphomedusae currently comprises 5 orders, 19 families, and about 202 species. These jellyfish are important pelagic predators at the center of concern about the "rise in gelatinous zooplankton" and degradation of coastal ecosystems. Previous phylogenetic relationship studies among Scyphomedusae species relied primarily on morphological data. However, morphology-based phylogeny and classification of this group are difficult due to the high diversity of morphological characters, and the topic remains controversial. Large molecular level advancements have yielded interesting results among the Scyphomedusae taxa. <i>Nemopilema nomurai</i>, <i>Rhopilema esculentum</i>, <i>Cyanea nozakii</i>, and <i>Aurelia </i>sp. are four common macro-jellyfish species in the Bohai and Yellow seas. In this study, the nuclear ITS-5.8S rDNA gene fragments from polyps, ephyrae, and adults of these species were amplified using polymerase chain reaction techniques. Homologous sequences of other Scyphomedusae jellyfish from GenBank were also included in this study. The genetic information indices, including base composition, sequence variation, and Kimura two-parameter genetic distance were examined. Phylogenetic trees were constructed based on the maximum-likelihood and Bayesian inference methods to determine the phylogenetic relationships among Scyphomedusae jellyfish. Significant length variations in the ITS-5.8S rDNA region were observed (length, 675-833 bp). A total of 886 aligned base pairs, with 507 variable sites and 197 parsimony informative sites, were detected in the four jellyfish species. Inter-individual internal transcribed spacer region (ITS)1 polymorphisms were observed in most of the Scyphomedusae jellyfish species(four families and nine species). Repeats in microsatellite ITS loci play an important role in length heteroplasmy. The genetic distances among families, species, and individuals were 0.295-0.491, 0.024-0.812, and 0-0.099, respectively. The phylogenic analysis showed that the topologies of the maximum-likelihood and Bayesian inference trees were somewhat different and different from morphological taxonomy. In conclusion, ITS is an appropriate barcoding tool to identify jellyfish species and classify young jellyfish. Furthermore, ITS1 was highly divergent among different Scyphomedusae jellyfish and could be an appropriate marker for molecular systematic studies at the species level. Additional in-depth studies with more samples are needed to further clarify the position of Scyphomedusae jellyfish in jellyfish taxonomy.