This chapter describes how neutral genetic markers can be used for the study of population and conservation genetics, phylogeography and gene flow in conifers. It includes a comprehensive review of the studies performed in these research fields. The chapter starts with a review of the different kinds of neutral genetic markers most frequently used in conifers in the recent literature. In the second part, it describes how variation is organized within and among natural population at the three conifer genomes (chloroplast, mitochondrial and nuclear). In the third part it highlights how stochastic processes have shaped this organization focusing on two large areas of investigation in population genetics: phylogeography and gene flow. Finally it demonstrates that neutral genetic markers and the information they generate are fundamental for the conservation and management of genetic resources. This chapter is addressed to plant molecular geneticists as well as plant breeders in the public and private sectors