Ecological genetics is the study of genetics and evolution 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 ecological genetics is on traits related to fitness, which affect an organism's survival and reproduction. Examples might be: flowering time, drought tolerance, polymorphism, mimicry, defence against predators.

Research usually involve a mixture of field and laboratory studies. Samples of natural populations may be taken back to the laboratory for their genetic variation to be analysed. Changes in the populations at different times and places will be noted, and the pattern of mortality in these populations will be studied. Research is often done on insects and other organisms that have short generation times.