Closely related species often differ in coloration. Understanding the mechanistic bases of such differences can reveal whether evolutionary changes in colour are driven by single key mechanisms or changes in multiple pathways. Non-iridescent structural plumage colours in birds are a good model in which to test these questions. These colours result from light absorption by pigments, light scattering by the medullary spongy layer (a nanostructure found within barbs) and contributions from other structural elements. Fairy-wrens (Malurus spp.) are a small clade of closely related birds that display a large diversity of ornamental structural colours. Using spectrometry, electron microscopy and Fourier analysis, we show that 30 structural colours, varying from ultraviolet to blue and purple, share a similar barb morphology. Despite this similarity, we find that at the microscopic scale, variation across multiple structural elements, including the size and density of the keratin cortex, spongy layer and melanin, explains colour diversity. These independent axes of morphological variation together account for sizeable amounts of structural colour variability (R-2 = 0.21-0.65). The coexistence of many independent, evolutionarily labile mechanisms that generate colour variation suggests that the diversity of structural colours in this clade could be mediated by many independent genetic and environmental factors.