Understanding the effects of interspecific competition on genetic diversity will deepen our knowledge on species evolution. In the case of Calopteryx splendens and C. virgo, sympatric damselfly species, interspecific interference competition by C. virgo has remarkable effects on territoriality of C. splendens resulting in reproductive character displacement. Since territoriality is correlated with phenotype and mating success, we investigated the effects of interspecific interference competition on genetic diversity of C. splendens populations. Using amplified fragment length polymorphisms (AFLP), we determined the population genetic structure of 12 C. splendens populations and used the genetic diversity information to relate heterozygosity of C. splendens to abundance of C. virgo in sympatric populations. We found that heterozygosity of C. splendens males decreased with increasing abundance of C. virgo males. This result most likely reflects changes in effective population size due to interspecific interference competition and shows an effect on genetic structure in damselfly populations.