生态遗传学（Ecological genetics）是研究生态学尺度的遗传学，主要关注于自然族群中的表现型的演化。群体遗传学为较为相关的其他学科。

Ecological genetics is the study of genetics in natural populations.

This contrasts with classical genetics, which works mostly on crosses between laboratory strains, and DNA sequence analysis, which studies genes at the molecular level.

Research in this field is on traits of ecological significance—that is, traits related to fitness, which affect an organism's survival and reproduction. Examples might be: flowering time, drought tolerance, polymorphism, mimicry, avoidance of attacks by predators.