While molecular and quantitative trait variation may be theoretically correlated, empirical studies using both approaches frequently reveal discordant patterns, and these discrepancies can contribute to our understanding of evolutionary processes. Here, we assessed genetic variation in six populations of the copepod Tigriopus californicus. Molecular variation was estimated using five polymorphic microsatellite loci, and quantitative variation was measured using 22-life history and morphometric characters. Within populations, no correlation was found between the levels of molecular variation (heterozygosity) and quantitative variation (heritability). Between populations, quantitative subdivision (Q(ST)) was correlated with molecular subdivision when measured as F(ST) but not when measured as R(ST). Unlike most taxa studied to date, the overall level of molecular subdivision exceeded the level of quantitative subdivision (F(ST) = 0.80, R(ST) = 0.89, Q(ST) = 0.30). Factors that could contribute to this pattern include stabilizing or fluctuating selection on quantitative traits or accelerated rates of molecular evolution.