Simple SummaryAphytis species (Hymenoptera: Aphelinidae) have been considered as the most important natural enemies in biological control of armoured scale insects (Hemiptera: Diaspididae). However, it is difficult to identify the species of the genus, particularly that of the A. lingnanensis group, based on adult morphological characters. Although the differences in pupal pigmentation of Aphytis species have been documented previously, they have not been much used as taxonomic characters for Aphytis species identification. In this study, we present four characteristic pigmentation patterns of Aphytis pupae, together with photographs, including the categories of: entirely yellow, partly dark brown, entirely or predominantly black, and partly black pupae. No significant intra-specific variation in pupal colour pattern was detected despite relatively high numbers of specimens examined, many from multiple, and different, origins. We summarize the present status of pupal pigmentation in the described species of Aphytis, according to the species groups, which could be used as an important supplementary diagnostic character for distinguishing species of Aphytis, especially closely-related species.Species identification of Aphytis on the basis of adult morphology is extremely difficult, especially in the A. lingnanensis group, with several cryptic species. Pupal pigmentation could be used as one of the taxonomic characters for Aphytis species, and in some instances, pupal pigmentation actually provided the first clue to the distinctness of cryptic Aphytis species. The present study investigated the full-grown larvae or younger pupae of Aphytis species, and pupal pigmentation and pupal development were observed and photographed. Four characteristic pigmentation patterns of Aphytis pupae were summarized including: entirely yellow, partly dark brown, entirely or predominantly black, and partly black. The species in the chilensis and mytilaspidis groups, and some unassigned species, generally have entirely, or predominantly and or partly black pupae. The species in the chrysomphali, funicularis, and proclia groups generally have the pupae entirely yellow. The species of the lingnanensis group have the pupae both entirely yellow, e.g., A. fisheri, and partly dark brown pupae, e.g., A. lingnanensis, A. holoxanthus and A. melinus. The pupae of Aphytis species in this study had a developmental duration of about 5–8 days at 27 ± 1 °C, 70 ± 5% RH and a photoperiod of 10L: 14D. It was found that the pupal skin was always melanized at the beginning stage, generally in the first day, among the pigmented pupae of Aphytis species. As development continued, the pigmentation became darker and the eye colour changed from pale red/brown to green. No significant intra-specific variation in pupal colour pattern was detected despite relatively high numbers of specimens examined, many from multiple, and different, origins. Overall, our study indicates that pupal pigmentation could be more helpful in species identification of Aphytis.