Natural hybridisation is widespread among coral reef fishes. However, the ecological promoters and evolutionary consequences of reef fish hybridisation have not been thoroughly evaluated. Butterflyfishes form a high number of hybrids and represent an appropriate group to investigate hybridisation in reef fishes. This study provides a rare test of terrestrially-derived hybridisation theory in the marine environment by examining hybridisation between Chaetodon trifasciatus and Chaetodon lunulatus at Christmas Island. Overlapping spatial and dietary ecologies enable heterospecific encounters. Non-assortative mating and local rarity of both parent species appear to permit heterospecific breeding pair formation. Microsatellite loci and mtDNA confirmed the status of hybrids, which displayed the lowest genetic diversity in the sample and used a reduced suite of resources, suggesting decreased adaptability. Maternal contribution to hybridisation was unidirectional, and no introgression was detected, suggesting limited, localised evolutionary consequences of hybridisation. Comparisons to other reef fish hybridisation studies revealed that different evolutionary consequences emerge, despite being promoted by similar factors, possibly due to the magnitude of genetic distance between hybridising species. This study highlights the need for further enquiry aimed at evaluating the importance and long-term consequences of reef fish hybridisation.