Abstract For neutral additive genes, the quantitative index of population divergence (QST) is equivalent to Wright’s fixation index (FST). Thus, divergent or convergent selection is usually invoked, respectively, as a cause of the observed increase (QST > FST) or decrease (QST < FST) of QST from its neutral expectation (QST = FST). However, neutral nonadditive gene action can mimic the additive expectations under selection. We have studied theoretically the effect of consecutive population bottlenecks on the difference FST - QST for two neutral biallelic epistatic loci, covering all types of marginal gene action. With simple dominance, QST < FST for only low to moderate frequencies of the recessive alleles; otherwise, QST > FST. Additional epistasis extends the condition QST < FST to a broader range of frequencies. Irrespective of the type of nonadditive action, QST < FST generally implies an increase of both the within-line additive variance after bottlenecks over its ancestral value (VA) and the between-line variance over its additive expectation (2FSTVA). Thus, both the redistribution of the genetic variance after bottlenecks and the FST - QST value are governed largely by the marginal properties of single loci. The results indicate that the use of the FST - QST criterion to investigate the relative importance of drift and selection in population differentiation should be restricted to pure additive traits.