Most species of the genus Eulecanium Cockerell (Hemiptera: Coccidae) are important economic pests for ornamental plants and fruit trees. Two morphologically similar species, Eulecanium giganteum Shinji and E. kuwanai Kanda, are distributed mainly in China and are quite difficult to identify because of the paucity of distinguishing characteristics, which can only be observed in slide-mounted young, adult females. Furthermore, we demonstrate here that the species occur in sympatry and on many of the same host plants. Mitochondrial cytochrome c oxidase I (COI) and the D2–D3 expansion segments of 28S rDNA were used for accurate identification of these two Eulecanium species from 19 different locations in China. The average K2P distances of COI sequences were 0.47% in E. kuwanai and 0.32% in E. giganteum, and the interspecific divergences varied from 7.23% to 8.34%. Neighbour-joining (NJ) trees of COI and 28S rDNA revealed two distinct non-overlapping clusters, respectively. Meanwhile, “best close match” analysis also showed that 100% of individuals were classified successfully using COI and 28 S sequences. Differentiating between E. giganteum and E. kuwanai is challenging when using ecological and morphological traits. In contrast, identification using DNA diagnostics appears to be very effective, especially when slide-mounted specimens are difficult to obtain.