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A genetic model is presented to explain plumage polymorphism in the Little Shag (Phalacrocorax melanoleucos brevirostris). Parent-offspring data from an Auckland colony show that expression of the three morphs (white-throated, smudgy and pied) is primarily controlled by two alleles at a single genetic locus. The allele specifying ‘dark’ (D) shows incomplete dominance over that specifying ‘pied’ (6). Comparison of morph frequencies with calculated genotype frequencies reveals that about 40% of white-throated birds are homozygous dominant (DD), the rest of the white-throated birds and all smudgy birds are heterozygous (Dd), and pied birds are homozygous recessive (dd). The population mates non-assortively and the Hardy-Weinberg law correctly predicts the frequencies of black and pied offspring from crosses. Morph frequencies (and allele ratios) show a gradient from north to south in New Zealand, dark birds being more common in the south. The main factor maintaining this cline may be climatic.