Mealybugs (Hemiptera: Pseudococcidae) are an insect group that feeds on plant sap; many are major pests of ornamental plants and crops worldwide. The difficulty of morphological identification of mealybugs points to a need for a rapid and effective identification method, like DNA barcoding, to assist morphological taxonomy. Here, we employed diverse methods (best close match [BCM], Neighbor-Joining [NJ] tree, Barcoding with LOGic formulas [BLOG], Poisson Tree Process [PTP] Species Delimitation Method) to test the efficiency of two molecular markers (mitochondrial cytochrome c oxidase I [COI] and large ribosomal subunit gene [28S]) that could be used for species identification of 54 mealybug species that commonly occur in China. Two hundred six COI barcodes (47 species) and 242 28S sequences (53 species) were recovered from 246 individuals. In both the COI and 28S data sets, species except for Planococcus citri and P. minor were unambiguously identified by all the methods. The PTP analysis based on COI sequences generated more putative species in Antonina tesquorum, Atrococcus paludinus, and Formicococcus sp. than morphological identification. Among these three cases, the sequences of At. paludinus showed 3.55% variation at the 28S locus, possibly reflecting cryptic diversity in this taxon. Our study corroborates the utility of the COI and 28S genes in the rapid identification of mealybugs, and the barcode library we provide will create an effective identification system for mealybug pest management in China.