Because mealybugs are one of the most economically damaging groups of insects on food crops and ornamental plants, some are regulated-species in quarantine with the foreign trade of agricultural products. However, the absence of morphological characteristics enabling the discrimination of early life stages often causes a significant delay or the rejection of a shipment when fruit is discovered containing them, causing much economic loss. A PCR-based method for species identification was developed for six mealybug species known from Korean pears including two regulated insects, Planococcus kraunhiae (Kuwana) and Crisicoccus matsumotoi (Siraiwa). Six sets of species-specific primers were designed based on the sequence comparison of the internal transcribed spacer 1 and 2 regions. Efficiency tests against many mealybug samples showed that this method could effectively discriminate different mealybug species regardless of their developmental stages. Blind tests against 11 field collected mealybug nymph samples indicated that a single PCR is enough to discriminate unidentified mealybugs collected on Korean pears. This new method will be useful in quarantine as well as pest monitoring by providing an easy, accurate way of identifying any life stage of these mealybugs.