The phenotype of a plant is a term used to describe observable characteristics, such as height, biomass, leaf shape and so on. We use the term phenotype in a more specific context to describe the collective expression of the genotype in conjunction with the environment on a plant's observable characteristics.

Plants of the same genotype interacting with the environment may manifest as different phenotypes. However, plants may have the same phenotype but different genotypes. This may occur in situations where:
I. A gene or genes display incomplete dominance (for example, if a plant is heterozygous for a gene and as a result its phenotype is intermediate to the two homozygous classes), the gene is said to be completely dominant if, for example, a lethal mutation that causes all plants in a population that have the mutation to die;
II. If a gene or genes associated with a phenotype are altered by the presence of modifiers, suppressors or other regulators produced by other genes (epistasis, epistatic interaction) such that the phenotype is altered;
III. If a certain combination of environmental conditions affects the relative expression of a gene or genes; or a combination of these factors that affects the relative expressivity of a gene of genes thus altering the degree to which the genotype manifests a phenotype.

We use different well defined phenotype measurements for specific traits (or defined characteristic, for example, seed germination rate) to quantify difference between individuals in a structured population.

Using replicated trials we can estimate the phenotypic variance for individuals in a population and partition this into the genetic and environmental variance components. This then allows us to gauge how well particular genotypes (individuals in the population) perform for a defined trait when grown in that environment. It is therefore possible and very desirable to gain an understanding of how well individuals perform for a particular trait in different growth environments.