Coral reef fishes exhibit extreme diversity in colouration, with many species being recognised as having colour polymorphism. While melanin-based colouration is known to occur in clownfishes (Pomacentridae), little is known about the frequency at which melanistic morphs occur in natural populations. The aim of this study was to assess the frequency of melanistic morphs in a coexisting population of nine clownfishes and to identify ecological covariates associated with morph distribution. In the Kavieng lagoonal system of Papua New Guinea (2°36ʹS, 150°46ʹE), melanistic morphs were found in Amphiprion chrysopterus (56 % of individuals), A. clarkii (29 %), A. percula (20 %), and A. polymnus (25 %) populations. A. leucokranos, A. melanopus, A. perideraion, A. sandaracinos, and Premnas biaculeatus populations were also surveyed, but were found to be without melanistic morphs. Unbiased recursive partitioning analyses identified a suite of interacting and conditional ecological factors encompassing social rank, host anemone species, and location effects as the primary factors predicting the distribution of melanistic morphs. Melanistic morphs were generally associated with host anemones from the genus Stichodactyla and with fish having a high social rank. The lack of a distinct melanistic morph locational ‘hot spot’ common to all species, despite locational coexistence, suggests that causative factors of location effects were different among species. Our results highlight the complexity of clownfish polymorphism associated with melanism, with multiple non-exclusive potential explanations identified for future investigation.