The noble scallop Chlamys nobilis is polymorphic in its shell colour, which includes orange, orange-purple, purple and brown. In this study, the inheritance of shell colours of this species was investigated by analysing shell colour segregation in juvenile scallops produced from cross-fertilization. Totally, twenty two families derived from four types of parental crosses were produced. The results clearly demonstrated that shell colour in this species was consistently inherited but insensitive to the environmental factors given that each family was maintained in a common environment. The pattern of the four superficial shell colours in C. nobilis appears to be genetically controlled by the interaction of one pair of nonallelic genes, with one locus showing dominance epistasis to the other one. One-locus-three-allele model was proposed to explain the genetic relationship of the orange-purple colour dominant to the purple and brown colours, and the purple colour dominant to the brown colour. While the phenotypic ratio of 12:3:1 detected in one specific family showed that the dominant allele of the other locus controlling orange colour may mask the effect of the locus controlling orange-purple, purple and brown colours. The present results provide a genetic basis for selective breeding in the noble scallop in terms of shell colour.