Inheritance is not always controlled by simple Mendelian genetics, in which one allele is completely dominant over a recessive allele; this is seen in two differing kinds of dominance, being incomplete dominance and codominance.

Incomplete dominance occurs when two different alleles are present, but neither allele is completely dominant. Both alleles contribute to the phenotype, but only partially; a third, intermediary phenotype can be observed. If a pure-breeding red rose is crossed with a pure-breeding white rose, then the F1 generation offspring will all have pink flowers. When these F1 pink roses are crossed, the F2 offspring have flowers in the ratio of 1:2:1, with 1 red, 2 pink and 1 white. This is termed incomplete dominance as one trait is not fully dominant over its partner, and the heterozygous phenotype (pink) is intermediate between the homozygous parental phenotypes (red and white). The notation is important when indicating incomplete inheritance patterns; a suitable upper-case letter designates the gene for the trait (e.g. C for colour) and upper-case superscript letter indicate the alleles shown in the punnet square below.

Codominance occurs when two alleles are completely dominant, and both alleles are expressed and observed in the phenotype. This is seen in certain coat colours in horses and cattle. Both alleles in the genotype are fully expressed in the heterozygote, and so traits are said to be codominant. In shorthorn cattle, alleles for coat colour are inherited in this way, and the two alleles are expressed as red coat and white coat. This is similar to the incomplete dominance shown in snapdragon flowers, but in this case, the offspring of the pure-breeding red and white parents have roan coats, which are a mixture of red and white hair.