One of the most challenging problems in evolutionary biology is linking the evolution of the phenotype with the underlying genotype, because most phenotypes are encoded by many genes that interact with each other and with the environment. Further, many phenotypes are correlated and selection on one can affect evolution of the other. This challenge is especially important in fishes, because their evolutionary response to harvest, global warming and conservation actions are among the least understood aspects of their management. Here, we discuss two major genetic approaches to studying the evolution of complex traits, multivariate quantitative genetics and molecular genetics, and examine the increasing interaction between the two fields. These interactions include using pedigree-based methods to study the evolution of multivariate traits in natural populations, comparing neutral and quantitative measures of population structure, and examining the contribution that the two approaches have made to each other. We then explore the major role that quantitative genetics is playing in two key issues in the conservation and management of fish populations: the evolutionary effects of fishing and adaptation to climate change. Throughout, we emphasize that it is important to anticipate the availability of improvements in molecular technology and statistical analyses by creating research populations such as inbred lines and families segregating at fitness traits, developing approaches to measuring the full range of phenotypes related to fitness, and collecting biological material and ecological data in natural populations. These steps will facilitate studies of the evolution of complex traits over informative temporal and spatial scales.