Understanding the molecular basis of adaptive traits is a major interest in conservation and population genetics. In commercial species, such as several conifers, it is also interesting for operational breeding. In this chapter, we provide a state-of-the-art view on candidate gene research, from general estimates of nucleotide diversity and recombination to new-generation neutrality tests and association genetics methodologies. Levels of nucleotide diversity in conifers are substantial, although lower than expected given their life-history traits. In addition, linkage disequilibrium seems to decay rapidly in this group of species, at least within genes that are not submitted to natural selection. These two facts makes genetic association studies appealing in conifers, as signifi cant associations may correspond to the actual causal polymorphisms. Population genomic methods also seem appropriate in conifers, in particular for those species with accused population genetic structure and strong response to environmental gradients. New-generation neutrality tests, outlier loci detection methods and genotype/phenotype association studies have revealed various candidate genes and single nucleotide polymorphisms underlying different adaptive phenotypes, despite potential confounding effects of demographical and historical processes. Finally, perspectives about future genomic research in conifers are provided, including its application for conservation and breeding.