Determining the molecular basis of heritable variation in complex, quantitative ecologically important traits will provide insight into the proximate mechanisms driving phenotypic and ecological variation, and the molecular evolutionary history of these traits. Furthermore, if the study organism is a “keystone species” whose presence or absence shapes ecological communities, then we extend our understanding of the effects of molecular variation to the level of communities. I examined the molecular basis of variation in 32 ecologically important traits in the freshwater pond keystone species Daphnia pulex, and identified thousands of candidate genes for which variation may affect not just Daphnia phenotypes, but the structure of communities. I extended the basic results to address two questions: what genes are associated with the offspring size-number trade-off in Daphnia; and can we identify candidate “keystone gene networks” for which variation may have a particularly strong influence on eco-evolutionary dynamics of limnetic communities? I found that different genes, with different biological functions, are associated with the trade-off in subsequent broods, and propose a model linking evolutionary frameworks to molecular biological functions. Next I found that quantitative genetic variation in keystone traits appears to co-vary with the selection regimes to which Daphnia is subject, and identified two candidate gene networks that may underpin this genetic variation. Not only do these results provide a host of molecular hypotheses to be tested as Daphnia matures as a model genomic organism, but they also suggest models that link molecular research with broader themes in ecology, evolution, and behavior. / text